Manual pages

Scope: User Contributed Perl Documentation.

[ Alias ↣ ] Name (section)	Brief
a2ping(1)	…
a2query(1)	Retrieve runtime configuration from a local Apache 2 HTTP server.
AAT(3)	Apache::ASP Toolkit module.
above(3pm)	Auto "use lib" when a module is in the tree of the PWD.
accessors(3pm)	Create accessor methods in caller's package.
accessors::chained(3pm)	Create method chaining accessors in caller's package.
accessors::classic(3pm)	Create 'classic' read/write accessor methods in caller's package.
accessors::ro(3pm)	Create 'classic' read-only accessor methods in caller's package.
accessors::rw(3pm)	Create 'classic' read/write accessor methods in caller's package.
acdcheck(1p)	…
Ace(3pm)	Object-Oriented Access to ACEDB Databases.
Ace::Browser::AceSubs(3pm)	Subroutines for AceBrowser.
Ace::Browser::LocalSiteDefs(3pm)	Master Configuration file for AceBrowser.
Ace::Browser::SearchSubs(3pm)	Subroutines for AceBrowser search scripts.
Ace::Browser::SiteDefs(3pm)	Access to AceBrowser configuration files.
Ace::Graphics::Fk(3pm)	A dummy feature object used for generating panel key tracks.
Ace::Graphics::Glyph(3pm)	Base class for Ace::Graphics::Glyph objects.
Ace::Graphics::Glyph::anchored_arrow(3pm)	The "anchored_arrow" glyph.
Ace::Graphics::Glyph::arrow(3pm)	The "arrow" glyph.
Ace::Graphics::Glyph::box(3pm)	The "box" glyph.
Ace::Graphics::Glyph::dot(3pm)	The "ellipse" glyph.
Ace::Graphics::Glyph::ex(3pm)	The "X" glyph.
Ace::Graphics::Glyph::graded_segments(3pm)	The "color-coded segments" glyph.
Ace::Graphics::Glyph::group(3pm)	The group glyph.
Ace::Graphics::Glyph::line(3pm)	The "line" glyph.
Ace::Graphics::Glyph::primers(3pm)	The "STS primers" glyph.
Ace::Graphics::Glyph::segments(3pm)	The "discontinuous segments" glyph.
Ace::Graphics::Glyph::span(3pm)	The "span" glyph.
Ace::Graphics::Glyph::toomany(3pm)	The "too many to show" glyph.
Ace::Graphics::Glyph::transcript(3pm)	The "gene" glyph.
Ace::Graphics::Glyph::triangle(3pm)	The "triangle" glyph.
Ace::Graphics::GlyphFactory(3pm)	Create Ace::Graphics::Glyphs.
Ace::Graphics::Panel(3pm)	PNG graphics of Ace::Sequence::Feature objects.
Ace::Graphics::Track(3pm)	PNG graphics of Ace::Sequence::Feature objects.
Ace::Iterator(3pm)	Iterate Across an ACEDB Query.
Ace::Local(3pm)	Use giface, tace or gifaceclient to open a local connection to an Ace database.
Ace::Model(3pm)	Get information about AceDB models.
Ace::Object(3pm)	Manipulate Ace Data Objects.
Ace::Sequence(3pm)	Examine ACeDB Sequence Objects.
Ace::Sequence::Feature(3pm)	Examine Sequence Feature Tables.
Ace::Sequence::FeatureList(3pm)	Lightweight Access to Features.
Ace::Sequence::GappedAlignment(3pm)	Gapped alignment object.
Ace::Sequence::Gene(3pm)	Simple "Gene" Object.
Ace::Sequence::Homol(3pm)	Temporary Sequence Homology Class.
Ace::Sequence::Multi(3pm)	Combine Feature Tables from Multiple Databases.
Ace::Sequence::Transcript(3pm)	Simple "Gene" Object.
acheck(1)	Check common localization mistakes.
acheck(5)	Acheck configuration file.
acheck-rules(5)	Rules set for acheck.
ack(1p)	Grep-like text finder.
ack-grep(1p) ↣ ack(1p)	Grep-like text finder.
Acme::Bleach(3pm)	For really clean programs.
Acme::Brainfuck(3pm)	Embed Brainfuck in your perl code.
Acme::constant(3pm)	Like constant, except actually not.
Acme::Damn(3pm)	'Unbless' Perl objects.
Acme::DWIM(3pm)	Perl's confusing operators made easy.
Acme::EyeDrops(3pm)	Visual Programming in Perl.
Acme::Morse(3pm)	Perl programming in morse code.
Acme::POE::Knee(3pm)	Time sliced pony race using the POE kernel.
AE(3pm)	Simpler/faster/newer/cooler AnyEvent API.
AFS::PAG(3pm)	Perl bindings for AFS PAG manipulation.
AI::FANN(3pm)	Perl wrapper for the Fast Artificial Neural Network library.
Alert.pm(3)	Octopussy Alert module.
alfilldb(1)	Add/update information of music files in the AudioLink database.
Algorithm::C3(3pm)	A module for merging hierarchies using the C3 algorithm.
Algorithm::CheckDigits(3pm)	Perl extension to generate and test check digits.
Algorithm::CheckDigits::M07_001(3pm)	Compute check digits modulo 7 method 1.
Algorithm::CheckDigits::M09_001(3pm)	Compute check digits for Euro notes.
Algorithm::CheckDigits::M10_001(3pm)	Compute check digits for Bahncard (DE), IMEI, IMEISV, ISIN, Miles&More, Payback (DE),.
Algorithm::CheckDigits::M10_002(3pm)	Compute check digits for CINS (US), SIREN (FR), SIRET (FR).
Algorithm::CheckDigits::M10_003(3pm)	Compute check digits for ISMN.
Algorithm::CheckDigits::M10_004(3pm)	Compute check digits for 2aus5, EAN, ILN, ISBN13, NVE.
Algorithm::CheckDigits::M10_005(3pm)	Compute check digits for Deutsche Post Identcode/Leitcode (DE).
Algorithm::CheckDigits::M10_006(3pm)	Compute check digits for Rentenversicherung (DE).
Algorithm::CheckDigits::M10_008(3pm)	Compute check digits for Sedol (GB).
Algorithm::CheckDigits::M10_009(3pm)	Compute check digits for Betriebsnummer (DE).
Algorithm::CheckDigits::M10_010(3pm)	Compute check digits for Postscheckkonti (CH).
Algorithm::CheckDigits::M10_011(3pm)	Compute check digits UPS (US).
Algorithm::CheckDigits::M11_001(3pm)	Compute check digits for ISBN, ISSN, VAT RN (PT), HKID (HK), Wagon number (BR), NHS.
Algorithm::CheckDigits::M11_002(3pm)	Compute check digits for PZN (DE).
Algorithm::CheckDigits::M11_003(3pm)	Compute check digits for PKZ (GDR).
Algorithm::CheckDigits::M11_004(3pm)	Compute check digits for CPF (BR), Titulo Eleitoral (BR).
Algorithm::CheckDigits::M11_006(3pm)	Compute check digits for Codigo de Cuenta Corriente (ES).
Algorithm::CheckDigits::M11_007(3pm)	Compute check digits for VAT Registration Number (FI).
Algorithm::CheckDigits::M11_008(3pm)	Compute check digits for VAT Registration Number (DK).
Algorithm::CheckDigits::M11_009(3pm)	Compute check digits NRIC (SG).
Algorithm::CheckDigits::M11_010(3pm)	Compute check digits AHV number (CH).
Algorithm::CheckDigits::M11_011(3pm)	Compute check digits for VAT Registration Number (NL).
Algorithm::CheckDigits::M11_012(3pm)	Compute check digits for Bundeswehrpersonenkennnummer (DE).
Algorithm::CheckDigits::M11_013(3pm)	Compute check digits for VAT Registration Number (GR).
Algorithm::CheckDigits::M11_015(3pm)	Compute check digits for ESR5 (CH).
Algorithm::CheckDigits::M11_016(3pm)	Compute check digits vor VAT Registration Number (PL).
Algorithm::CheckDigits::M11_017(3pm)	Compute check digits for EC-No, EINECS, ELINCS.
Algorithm::CheckDigits::M16_001(3pm)	Compute check digits for ISAN.
Algorithm::CheckDigits::M23_001(3pm)	Compute check digits for DNI (ES).
Algorithm::CheckDigits::M23_002(3pm)	Compute check digits for VAT Registration Number (IE).
Algorithm::CheckDigits::M43_001(3pm)	Compute check digits for Code-39.
Algorithm::CheckDigits::M89_001(3pm)	Compute check digits for VAT Registration Number (LU).
Algorithm::CheckDigits::M97_001(3pm)	Compute check digits for VAT Registration Number (BE).
Algorithm::CheckDigits::M97_002(3pm)	Compute check digits for International Bank Account Number (IBAN).
Algorithm::CheckDigits::MBase_001(3pm)	Compute check digits for UPC (US).
Algorithm::CheckDigits::MBase_002(3pm)	Compute check digits for blood bags (DE), BZUe (DE), VAT Registration Number (DE).
Algorithm::CheckDigits::MBase_003(3pm)	Compute check digits for SICI (Serial Item and Contribution Identifier).
Algorithm::CheckDigits::MXX_001(3pm)	Compute check digits for PA (DE).
Algorithm::CheckDigits::MXX_002(3pm)	Compute check digits for CAS.
Algorithm::CheckDigits::MXX_003(3pm)	Compute check digits for DEM.
Algorithm::CheckDigits::MXX_004(3pm)	Compute check digits for VAT RN (AT).
Algorithm::CheckDigits::MXX_005(3pm)	Compute check digits for ESR9 (CH).
Algorithm::CheckDigits::MXX_006(3pm)	Compute check digits with Verhoeff scheme.
Algorithm::Combinatorics(3pm)	Efficient generation of combinatorial sequences.
Algorithm::Dependency(3pm)	Base class for implementing various dependency trees.
Algorithm::Dependency::Item(3pm)	Implements an item in a dependency heirachy.
Algorithm::Dependency::Ordered(3pm)	Implements an ordered dependency heirachy.
Algorithm::Dependency::Source(3pm)	Implements a source of heirachy items.
Algorithm::Dependency::Source::File(3pm)	File source for dependency heirachys.
Algorithm::Dependency::Source::HoA(3pm)	Source for a HASH of ARRAYs.
Algorithm::Dependency::Source::Invert(3pm)	Logically invert a source.
Algorithm::Dependency::Weight(3pm)	Calculate dependency 'weights'.
Algorithm::Diff(3pm)	Compute `intelligent' differences between two files / lists.
Algorithm::Diff::XS(3pm)	Algorithm::Diff with XS core loop.
Algorithm::DiffOld(3pm)	Compute `intelligent' differences between two files / lists but use the old (.
Algorithm::LBFGS(3pm)	Perl extension for L-BFGS.
Algorithm::Merge(3pm)	Three-way merge and diff.
Algorithm::Munkres(3pm)	Perl extension for Munkres' solution to.
Algorithm::Numerical::Sample(3pm)	Draw samples from a set.
Algorithm::Permute(3pm)	Handy and fast permutation with object oriented interface.
algotutor(1)	An interactive program for observing the intermediate steps of algorithms.
Alias(3pm)	Declare symbolic aliases for perl data.
aliased(3pm)	Use shorter versions of class names.
alien(1p)	Convert or install an alien binary package.
Alien::Gnuplot(3pm)	Find and verify functionality of the gnuplot executable.
Alien::Package(3pm)	An object that represents a package.
Alien::Package::Deb(3pm)	An object that represents a deb package.
Alien::Package::Lsb(3pm)	An object that represents a lsb package.
Alien::Package::Pkg(3pm)	An object that represents a Solaris pkg package.
Alien::Package::Rpm(3pm)	An object that represents a rpm package.
Alien::Package::Slp(3pm)	An object that represents a slp package.
Alien::Package::Tgz(3pm)	An object that represents a tgz package.
Alien::SDL(3pm)	Building, finding and using SDL binaries.
Alien::SDL::ConfigData(3pm)	Configuration for Alien::SDL.
Alien::wxWidgets(3pm)	Building, finding and using wxWidgets binaries.
Alien::wxWidgets::Utility(3pm)	INTERNAL: do not use.
align2kog.pl(1)	Converts an alignment into a kog file.
all-knowing-dns(1p)	Tiny DNS server for IPv6 Reverse DNS.
alsearch(1)	Search the AudioLink database for music.
Alt(3pm)	Alternate Module Implementations.
Alt::Assert(3pm)	Assert alternate module implementation.
Alt::Base(3pm)	Base class for alternate module.
altree(1p)	Association and Localisation tests using phylogenetic Trees.
altree-add-S(1p)	Title...
altree-convert(1p)	Title...
ALTree::CUtils(3pm)	Perl extension for blah blah blah.
Alzabo(3pm)	A data modelling tool and RDBMS-OO mapper.
Alzabo::BackCompat(3pm)	Convert old data structures.
Alzabo::ChangeTracker(3pm)	Saves a set of changes as callbacks that can be backed out if needed.
Alzabo::Column(3pm)	Column objects.
Alzabo::ColumnDefinition(3pm)	Holds the type attribute for a column.
Alzabo::Config(3pm)	Alzabo configuration information.
Alzabo::Create(3pm)	Loads all Alzabo::Create::* classes.
Alzabo::Create::Column(3pm)	Column objects for use in schema creation.
Alzabo::Create::ColumnDefinition(3pm)	Column definition object for schema creation.
Alzabo::Create::ForeignKey(3pm)	Foreign key objects for schema creation.
Alzabo::Create::Index(3pm)	Index objects for schema creation.
Alzabo::Create::Schema(3pm)	Schema objects for schema creation.
Alzabo::Create::Table(3pm)	Table objects for schema creation.
Alzabo::Debug(3pm)	Creates constants used to turn on debugging.
Alzabo::Design(3pm)	Documentation on Alzabo's design.
Alzabo::Driver(3pm)	Alzabo base class for RDBMS drivers.
Alzabo::Driver::MySQL(3pm)	MySQL specific Alzabo driver subclass.
Alzabo::Driver::PostgreSQL(3pm)	PostgreSQL specific Alzabo driver subclass.
Alzabo::Exceptions(3pm)	Creates all exception subclasses used in Alzabo.
Alzabo::FAQ(3pm)	Frequently Asked Questions.
Alzabo::ForeignKey(3pm)	Foreign key (relation) objects.
Alzabo::Index(3pm)	Index objects.
Alzabo::Intro(3pm)	Introductory information about Alzabo.
Alzabo::MethodMaker(3pm)	Auto-generate useful methods based on an existing schema.
Alzabo::MySQL(3pm)	Alzabo and MySQL.
Alzabo::PostgreSQL(3pm)	Alzabo and PostgreSQL.
Alzabo::QuickRef(3pm)	A quick reference to methods in the Alzabo classes.
Alzabo::RDBMSRules(3pm)	Base class for Alzabo RDBMS rulesets.
Alzabo::RDBMSRules::MySQL(3pm)	MySQL specific database rules.
Alzabo::RDBMSRules::PostgreSQL(3pm)	PostgreSQL specific database rules.
Alzabo::Runtime(3pm)	Loads all Alzabo::Runtime::* classes.
Alzabo::Runtime::Column(3pm)	Column objects.
Alzabo::Runtime::ColumnDefinition(3pm)	Column definition objects.
Alzabo::Runtime::Cursor(3pm)	Base class for Alzabo cursors.
Alzabo::Runtime::ForeignKey(3pm)	Foreign key objects.
Alzabo::Runtime::Index(3pm)	Index objects.
Alzabo::Runtime::InsertHandle(3pm)	A handle representing an insert.
Alzabo::Runtime::JoinCursor(3pm)	Cursor that returns arrays of "Alzabo::Runtime::Row" objects.
Alzabo::Runtime::Row(3pm)	Row objects.
Alzabo::Runtime::RowCursor(3pm)	Cursor that returns "Alzabo::Runtime::Row" objects.
Alzabo::Runtime::RowState::Deleted(3pm)	Row objects that have been deleted.
Alzabo::Runtime::RowState::InCache(3pm)	Cached row objects that represent actual database rows.
Alzabo::Runtime::RowState::Live(3pm)	Row objects representing rows in the database.
Alzabo::Runtime::RowState::Potential(3pm)	Row objects that are not in the database.
Alzabo::Runtime::Schema(3pm)	Schema objects.
Alzabo::Runtime::Table(3pm)	Table objects.
Alzabo::Runtime::UniqueRowCache(3pm)	Implements a row cache for Alzabo.
Alzabo::Schema(3pm)	Schema objects.
Alzabo::SQLMaker(3pm)	Alzabo base class for RDBMS drivers.
Alzabo::SQLMaker::MySQL(3pm)	Alzabo SQL making class for MySQL.
Alzabo::SQLMaker::PostgreSQL(3pm)	Alzabo SQL making class for PostgreSQL.
Alzabo::Table(3pm)	Table objects.
Alzabo::Utils(3pm)	Utility functions for other Alzabo modules.
Amazon::SQS::Simple(3pm)	OO API for accessing the Amazon Simple Queue Service.
Amazon::SQS::Simple::Base(3pm)	No user-serviceable parts included.
Amazon::SQS::Simple::Message(3pm)	OO API for representing messages from the Amazon Simple Queue Service.
Amazon::SQS::Simple::Queue(3pm)	OO API for representing queues from the Amazon Simple Queue Service.
Amazon::SQS::Simple::SendResponse(3pm)	OO API for representing responses to messages sent to the Amazon Simple.
analyze-pat.pl(1)	…
Any::Moose(3pm)	(DEPRECATED) use Moo instead!.
Any::Template::ProcessDir(3pm)	…
Any::URI::Escape(3pm)	Load URI::Escape::XS preferentially over URI::Escape.
AnyData(3pm)	(DEPRECATED) easy access to data in many formats.
AnyData::Format::CSV(3pm)	Tiedhash & DBI/SQL access to CSV data.
AnyData::Format::Fixed(3pm)	Tiedhash & DBI/SQL access to Fixed length data.
AnyData::Format::HTMLtable(3pm)	Tied hash and DBI/SQL access to HTML tables.
AnyData::Format::Ini(3pm)	Tiedhash & DBI/SQL access to ini files.
AnyData::Format::Mp3(3pm)	Tied hash and DBI access to Mp3 files.
AnyData::Format::Paragraph(3pm)	Tiedhash & DBI/SQL access to vertical files.
AnyData::Format::Passwd(3pm)	Tied hash and DBI access to passwd files.
AnyData::Format::Pipe(3pm)	Tiedhash & DBI/SQL access to Pipe delimited files.
AnyData::Format::Tab(3pm)	Tiedhash & DBI/SQL access to Tab delimited files.
AnyData::Format::Weblog(3pm)	Tiedhash & DBI/SQL access to HTTPD Logs.
AnyData::Format::XML(3pm)	Tiedhash and DBI access to XML.
AnyData::Storage::File(3pm)	…
AnyEvent(3pm)	The DBI of event loop programming.
AnyEvent::AggressiveIdle(3pm)	Aggressive idle processes for AnyEvent.
AnyEvent::CacheDNS(3pm)	Simple DNS resolver with caching.
AnyEvent::Callback(3pm)	Callback aggregator for AnyEvent watchers.
AnyEvent::Connection(3pm)	Base class for tcp connectful clients.
AnyEvent::DBD::Pg(3pm)	AnyEvent interface to DBD::Pg's async interface.
AnyEvent::DBI(3pm)	Asynchronous DBI access.
AnyEvent::Debug(3pm)	Debugging utilities for AnyEvent.
AnyEvent::DNS(3pm)	Fully asynchronous DNS resolution.
AnyEvent::FAQ(3pm)	Frequently asked questions.
AnyEvent::ForkObject(3pm)	Async access on objects.
AnyEvent::Gearman(3pm)	Asynchronous Gearman client/worker module for AnyEvent applications.
AnyEvent::Gearman::Client(3pm)	Gearman client for AnyEvent application.
AnyEvent::Gearman::Client::Connection(3pm)	Connection class for client.
AnyEvent::Gearman::Connection(3pm)	Common base class to handle connection.
AnyEvent::Gearman::Constants(3pm)	Constants for Gearman client/worker.
AnyEvent::Gearman::Job(3pm)	Gearman job.
AnyEvent::Gearman::Task(3pm)	Gearman task.
AnyEvent::Gearman::Types(3pm)	Some subtype definitions.
AnyEvent::Gearman::Worker(3pm)	Gearman worker for AnyEvent application.
AnyEvent::Gearman::Worker::Connection(3pm)	Connection class for worker.
AnyEvent::Handle(3pm)	Non-blocking I/O on streaming handles via AnyEvent.
AnyEvent::Handle::UDP(3pm)	Client/server UDP handles for AnyEvent.
AnyEvent::HTTP(3pm)	Simple but non-blocking HTTP/HTTPS client.
AnyEvent::HTTP::ScopedClient(3pm)	AnyEvent based.
AnyEvent::HTTPD(3pm)	A simple lightweight event based web (application) server.
AnyEvent::HTTPD::HTTPConnection(3pm)	A simple HTTP connection for request and response handling.
AnyEvent::HTTPD::HTTPServer(3pm)	A simple and plain http server.
AnyEvent::HTTPD::Request(3pm)	A web application request handle for AnyEvent::HTTPD.
AnyEvent::HTTPD::Util(3pm)	Utility functions for AnyEvent::HTTPD.
AnyEvent::I3(3pm)	Communicate with the i3 window manager.
AnyEvent::Impl::Cocoa(3pm)	AnyEvent adaptor for Cocoa::EventLoop.
AnyEvent::Impl::EV(3pm)	AnyEvent adaptor for EV.
AnyEvent::Impl::Event(3pm)	AnyEvent adaptor for Event.
AnyEvent::Impl::EventLib(3pm)	AnyEvent adaptor for Event::Lib.
AnyEvent::Impl::FLTK(3pm)	AnyEvent adaptor for FLTK (Fast Light Toolkit version two).
AnyEvent::Impl::Glib(3pm)	AnyEvent adaptor for Glib.
AnyEvent::Impl::IOAsync(3pm)	AnyEvent adaptor for IO::Async.
AnyEvent::Impl::Irssi(3pm)	AnyEvent adaptor for Irssi.
AnyEvent::Impl::Perl(3pm)	AnyEvent adaptor for AnyEvent's pure perl AnyEvent::Loop.
AnyEvent::Impl::POE(3pm)	AnyEvent adaptor for POE.
AnyEvent::Impl::Qt(3pm)	AnyEvent adaptor for Qt.
AnyEvent::Impl::Tk(3pm)	AnyEvent adaptor for Tk.
AnyEvent::Impl::UV(3pm)	AnyEvent adaptor for UV.
AnyEvent::Intro(3pm)	An introductory tutorial to AnyEvent.
AnyEvent::IO(3pm)	The DBI of asynchronous I/O implementations.
AnyEvent::IO::IOAIO(3pm)	AnyEvent::IO backend based on IO::AIO.
AnyEvent::IO::Perl(3pm)	Pure perl backend for AnyEvent::IO.
AnyEvent::IRC(3pm)	An event based IRC protocol client API.
AnyEvent::IRC::Client(3pm)	A highlevel IRC connection.
AnyEvent::IRC::Connection(3pm)	An IRC connection abstraction.
AnyEvent::IRC::Util(3pm)	Common utilities that help with IRC protocol handling.
AnyEvent::Log(3pm)	Simple logging "framework".
AnyEvent::Loop(3pm)	AnyEvent's Pure-Perl event loop.
AnyEvent::Memcached(3pm)	AnyEvent memcached client.
AnyEvent::Memcached::Hash::WithNext(3pm)	Hashing algorythm for AE::Memcached.
AnyEvent::Processor(3pm)	Base class to define an event-driven (AnyEvent) task that could periodically be.
AnyEvent::Processor::Conversion(3pm)	Base class for conversion type subclasses.
AnyEvent::Processor::Converter(3pm)	Role for any converter class.
AnyEvent::Processor::WatchableTask(3pm)	Role for tasks which are watchable.
AnyEvent::Processor::Watcher(3pm)	A watcher echoing a process messages, base class.
AnyEvent::RabbitMQ(3pm)	An asynchronous and multi channel Perl AMQP client.
AnyEvent::RabbitMQ::Channel(3pm)	Abstraction of an AMQP channel.
AnyEvent::README(3pm)	Callback aggregator for AnyEvent watchers.
AnyEvent::Redis(3pm)	Non-blocking Redis client.
AnyEvent::Redis::Protocol(3pm)	Redis response parser (read handler) for AnyEvent.
AnyEvent::Serialize(3pm)	Async serialize/deserialize function.
AnyEvent::Socket(3pm)	Useful IPv4 and IPv6 stuff. also unix domain sockets. and stuff.
AnyEvent::Strict(3pm)	Force strict mode on for the whole process.
AnyEvent::TermKey(3pm)	Terminal key input using "libtermkey" with "AnyEvent".
AnyEvent::TLS(3pm)	SSLv2/SSLv3/TLSv1 contexts for use in AnyEvent::Handle.
AnyEvent::Tools(3pm)	Instrument collection for AnyEvent.
AnyEvent::Util(3pm)	Various utility functions.
AnyEvent::XMPP(3pm)	An implementation of the XMPP Protocol.
AnyEvent::XMPP::Client(3pm)	XMPP Client abstraction.
AnyEvent::XMPP::Component(3pm)	"XML" stream that implements the XEP-0114.
AnyEvent::XMPP::Connection(3pm)	XML stream that implements the XMPP RFC 3920.
AnyEvent::XMPP::Error(3pm)	Error class hierarchy for error reporting.
AnyEvent::XMPP::Error::Exception(3pm)	Some exception was thrown somewhere.
AnyEvent::XMPP::Error::IQ(3pm)	IQ errors.
AnyEvent::XMPP::Error::IQAuth(3pm)	IQ authentication error.
AnyEvent::XMPP::Error::Message(3pm)	Message errors.
AnyEvent::XMPP::Error::MUC(3pm)	MUC error.
AnyEvent::XMPP::Error::Parser(3pm)	XML parse errors.
AnyEvent::XMPP::Error::Presence(3pm)	Presence errors.
AnyEvent::XMPP::Error::Register(3pm)	In-band registration error.
AnyEvent::XMPP::Error::SASL(3pm)	SASL authentication error.
AnyEvent::XMPP::Error::Stanza(3pm)	Stanza errors.
AnyEvent::XMPP::Error::Stream(3pm)	XML Stream errors.
AnyEvent::XMPP::Ext(3pm)	Extension baseclass and documentation.
AnyEvent::XMPP::Ext::DataForm(3pm)	XEP-0004 DataForm.
AnyEvent::XMPP::Ext::Disco(3pm)	Service discovery manager class for XEP-0030.
AnyEvent::XMPP::Ext::Disco::Info(3pm)	Service discovery info.
AnyEvent::XMPP::Ext::Disco::Items(3pm)	Service discovery items.
AnyEvent::XMPP::Ext::MUC(3pm)	Implements XEP-0045: Multi-User Chat.
AnyEvent::XMPP::Ext::MUC::Message(3pm)	A room message.
AnyEvent::XMPP::Ext::MUC::Room(3pm)	Room class.
AnyEvent::XMPP::Ext::MUC::RoomInfo(3pm)	Room information.
AnyEvent::XMPP::Ext::MUC::User(3pm)	User class.
AnyEvent::XMPP::Ext::OOB(3pm)	XEP-0066 Out of Band Data.
AnyEvent::XMPP::Ext::Ping(3pm)	Implementation of XMPP Ping XEP-0199.
AnyEvent::XMPP::Ext::Pubsub(3pm)	Implements XEP-0060: Publish-Subscribe.
AnyEvent::XMPP::Ext::Receipts(3pm)	XEP-0184 message receipts.
AnyEvent::XMPP::Ext::RegisterForm(3pm)	Handle for in band registration.
AnyEvent::XMPP::Ext::Registration(3pm)	Handles all tasks of in band registration.
AnyEvent::XMPP::Ext::VCard(3pm)	VCards (XEP-0054 & XEP-0084).
AnyEvent::XMPP::Ext::Version(3pm)	Software version.
AnyEvent::XMPP::Extendable(3pm)	Extendable baseclass.
AnyEvent::XMPP::IM::Account(3pm)	Instant messaging account.
AnyEvent::XMPP::IM::Connection(3pm)	"XML" stream that implements the XMPP RFC 3921.
AnyEvent::XMPP::IM::Contact(3pm)	Instant messaging roster contact.
AnyEvent::XMPP::IM::Delayed(3pm)	A delayed "XML" stanza.
AnyEvent::XMPP::IM::Message(3pm)	Instant message.
AnyEvent::XMPP::IM::Presence(3pm)	XMPP presence.
AnyEvent::XMPP::IM::Roster(3pm)	Instant messaging roster for XMPP.
AnyEvent::XMPP::Namespaces(3pm)	XMPP namespace collection and aliasing class.
AnyEvent::XMPP::Node(3pm)	XML node tree helper for the parser.
AnyEvent::XMPP::Parser(3pm)	Parser for XML streams (helper for AnyEvent::XMPP).
AnyEvent::XMPP::SimpleConnection(3pm)	Low level TCP/TLS connection.
AnyEvent::XMPP::TestClient(3pm)	XMPP Test Client for tests.
AnyEvent::XMPP::Util(3pm)	Utility functions for AnyEvent::XMPP.
AnyEvent::XMPP::Writer(3pm)	"XML" writer for XMPP.
Apache2::Access(3pm)	A Perl API for Apache request object: Access, Authentication and Authorization.
Apache2::AuthCASSimple(3pm)	Apache2 module to authentificate through a CAS server.
Apache2::AuthCookie(3pm)	Perl Authentication and Authorization via cookies.
Apache2::AuthCookie::Params(3pm)	AuthCookie Params Driver for mod_perl 2.x.
Apache2::AuthenNTLM(3pm)	Perform Microsoft NTLM and Basic User Authentication.
Apache2::Build(3pm)	Methods for locating and parsing bits of Apache source code.
Apache2::CmdParms(3pm)	Perl API for Apache command parameters object.
Apache2::Command(3pm)	Perl API for accessing Apache module command information.
Apache2::compat(3pm)	…
Apache2::Connection(3pm)	Perl API for Apache connection object.
Apache2::ConnectionUtil(3pm)	Perl API for Apache connection utils.
Apache2::Const(3pm)	Perl Interface for Apache Constants.
Apache2::Cookie(3pm)	HTTP Cookies Class.
Apache2::Directive(3pm)	Perl API for manipulating the Apache configuration tree.
Apache2::Filter(3pm)	Perl API for Apache 2.0 Filtering.
Apache2::FilterRec(3pm)	Perl API for manipulating the Apache filter record.
Apache2::HookRun(3pm)	Perl API for Invoking Apache HTTP phases.
Apache2::Log(3pm)	Perl API for Apache Logging Methods.
Apache2::Module(3pm)	Perl API for creating and working with Apache modules.
Apache2::MPM(3pm)	Perl API for accessing Apache MPM information.
Apache2::PerlSections(3pm)	Write Apache configuration files in Perl.
Apache2::porting(3pm)	…
Apache2::Process(3pm)	Perl API for Apache process record.
Apache2::Reload(3pm)	Reload Perl Modules when Changed on Disk.
Apache2::Request(3pm)	Methods for dealing with client request data.
Apache2::RequestIO(3pm)	Perl API for Apache request record IO.
Apache2::RequestRec(3pm)	Perl API for Apache request record accessors.
Apache2::RequestUtil(3pm)	Perl API for Apache request record utils.
Apache2::Resource(3pm)	Limit resources used by httpd children.
Apache2::Response(3pm)	Perl API for Apache HTTP request response methods.
Apache2::ServerRec(3pm)	Perl API for Apache server record accessors.
Apache2::ServerUtil(3pm)	Perl API for Apache server record utils.
Apache2::SiteControl(3pm)	Perl web site authentication/authorization system.
Apache2::SiteControl::GrantAllRule(3pm)	A rule that grants permission to do everything.
Apache2::SiteControl::ManagerFactory(3pm)	An abstract base class to use as a pattern for custom PermissionManager.
Apache2::SiteControl::PermissionManager(3pm)	Rule-based permission management.
Apache2::SiteControl::Radius(3pm)	Raduis authentication module for SiteControl.
Apache2::SiteControl::Rule(3pm)	Permission manager access rule.
Apache2::SiteControl::User(3pm)	User representations.
Apache2::SiteControl::UserFactory(3pm)	User factory/persistence.
Apache2::SizeLimit(3pm)	Because size does matter.
Apache2::Status(3pm)	Embedded interpreter status information.
Apache2::SubProcess(3pm)	…
Apache2::SubRequest(3pm)	Perl API for Apache subrequests.
Apache2::Upload(3pm)	Methods for dealing with file uploads.
Apache2::URI(3pm)	Perl API for manipulating URIs.
Apache2::Util(3pm)	Perl API for Misc Apache Utility functions.
Apache2_4::AuthCookie(3pm)	Perl Authentication and Authorization via cookies for Apache 2.4.
Apache::Admin::Config(3pm)	A module to read/write Apache like configuration files.
Apache::ASP(3pm)	Active Server Pages for Apache with mod_perl.
Apache::ASP::CGI::Table(3pm)	Layer for compatibility with Apache::Table objects.
Apache::AuthCookie(3pm)	Perl Authentication and Authorization via cookies.
Apache::AuthCookie::Autobox(3pm)	Autobox Extensions for AuthCookie.
Apache::AuthCookie::FAQ(3pm)	Frequently Asked Questions about Apache::AuthCookie.
Apache::AuthCookie::Params(3pm)	AuthCookie Params Driver for mod_perl 1.x.
Apache::AuthCookie::Params::Base(3pm)	Internal CGI AuthCookie Params Base Class.
Apache::AuthCookie::Params::CGI(3pm)	Internal CGI Params Subclass.
Apache::AuthCookie::Util(3pm)	Internal Utility Functions for AuthCookie.
Apache::AuthDBI(3pm)	Authentication and Authorization via Perl's DBI.
Apache::AuthenHook(3pm)	Perl API for Apache 2.1 authentication.
Apache::AuthzNetLDAP(3pm)	Apache-Perl module that enables you to authorize a user for Website based on LDAP.
Apache::DB(3pm)	Run the interactive Perl debugger under mod_perl.
Apache::DBI(3pm)	Initiate a persistent database connection.
Apache::DBILogger(3pm)	Tracks what's being transferred in a DBI database.
Apache::DProf(3pm)	Hook Devel::DProf into mod_perl.
Apache::ePerl(3pm)	Fast emulated Embedded Perl (ePerl) facility.
Apache::Gallery(3pm)	Mod_perl handler to create an image gallery.
Apache::Htgroup(3pm)	Manage Apache authentication group files.
Apache::Htpasswd(3pm)	Manage Unix crypt-style password file.
Apache::LogFormat::Compiler(3pm)	Compile a log format string to perl-code.
Apache::perl5db(3pm)	The perl debugger.
Apache::Qpsmtpd(3pm)	A mod_perl-2 connection handler for qpsmtpd.
Apache::Session(3pm)	A persistence framework for session data.
Apache::Session::Browseable(3pm)	Add index and search methods to Apache::Session.
Apache::Session::Browseable::LDAP(3pm)	An implementation of Apache::Session::LDAP.
Apache::Session::Browseable::MySQL(3pm)	Add index and search methods to Apache::Session::MySQL.
Apache::Session::Browseable::Redis(3pm)	Add index and search methods to Apache::Session::Redis.
Apache::Session::Browseable::SQLite(3pm)	An implementation of Apache::Session.
Apache::Session::Browseable::Store::LDAP(3pm)	Use LDAP to store persistent objects.
Apache::Session::Browseable::Store::Redis(3pm)	An implementation of Apache::Session::Store.
Apache::Session::Browseable::Store::SQLite(3pm)	Store persistent data in a SQLite database.
Apache::Session::DB_File(3pm)	An implementation of Apache::Session.
Apache::Session::File(3pm)	An implementation of Apache::Session.
Apache::Session::Flex(3pm)	Specify everything at runtime.
Apache::Session::Generate::MD5(3pm)	Use MD5 to create random object IDs.
Apache::Session::Generate::ModUniqueId(3pm)	Mod_unique_id for session ID generation.
Apache::Session::Generate::ModUsertrack(3pm)	Mod_usertrack for session ID generation.
Apache::Session::Informix(3pm)	An implementation of Apache::Session.
Apache::Session::LDAP(3pm)	An implementation of Apache::Session.
Apache::Session::Lock::File(3pm)	Provides mutual exclusion using flock.
Apache::Session::Lock::MySQL(3pm)	Provides mutual exclusion using MySQL.
Apache::Session::Lock::Null(3pm)	Does not actually provides mutual exclusion.
Apache::Session::Lock::Semaphore(3pm)	Provides mutual exclusion through semaphores.
Apache::Session::Lock::Sybase(3pm)	Provides mutual exclusion using Sybase.
Apache::Session::Memcached(3pm)	Stores persistent data using memcached (memory cache daemon) for Apache::Session.
Apache::Session::MySQL(3pm)	An implementation of Apache::Session.
Apache::Session::MySQL::NoLock(3pm)	An implementation of Apache::Session::MySQL without locking.
Apache::Session::Oracle(3pm)	An implementation of Apache::Session.
Apache::Session::Postgres(3pm)	An implementation of Apache::Session.
Apache::Session::Serialize::Base64(3pm)	Use Storable and MIME::Base64 to zip up persistent data.
Apache::Session::Serialize::Storable(3pm)	Use Storable to zip up persistent data.
Apache::Session::Serialize::Sybase(3pm)	Use Storable to zip up persistent data and unpack/pack to put into.
Apache::Session::Serialize::UUEncode(3pm)	Use Storable and "pack()" to zip up persistent data.
Apache::Session::Store::DB_File(3pm)	Use DB_File to store persistent objects.
Apache::Session::Store::File(3pm)	Store persistent data on the filesystem.
Apache::Session::Store::Informix(3pm)	Store persistent data in a Informix database.
Apache::Session::Store::LDAP(3pm)	Use LDAP to store persistent objects.
Apache::Session::Store::Memcached(3pm)	Stores persistent data using memcached (memory cache daemon) for.
Apache::Session::Store::MySQL(3pm)	Store persistent data in a MySQL database.
Apache::Session::Store::Oracle(3pm)	Store persistent data in a Oracle database.
Apache::Session::Store::Postgres(3pm)	Store persistent data in a Postgres database.
Apache::Session::Store::Sybase(3pm)	Store persistent data in a Sybase database.
Apache::Session::Sybase(3pm)	An implementation of Apache::Session.
Apache::Session::Wrapper(3pm)	A simple wrapper around Apache::Session.
Apache::SessionX(3pm)	An extented persistence framework for session data.
Apache::SessionX::Generate::MD5(3pm)	Use MD5 to create random object IDs.
Apache::Singleton(3pm)	Singleton class for mod_perl.
Apache::Singleton::Process(3pm)	One instance per One Process.
Apache::Singleton::Request(3pm)	One instance per One Request.
Apache::SizeLimit::Core(3pm)	Because size does matter.
Apache::SmallProf(3pm)	Hook Devel::SmallProf into mod_perl.
Apache::SOAP(3pm)	Mod_perl-based SOAP server with minimum configuration.
Apache::SSLLookup(3pm)	Hooks for various mod_ssl functions.
Apache::Test(3pm)	Test.pm wrapper with helpers for testing Apache.
Apache::TestConfig(3pm)	…
Apache::TestHandler(3pm)	A few response handlers and helpers.
Apache::TestMB(3pm)	Subclass of Module::Build to support Apache::Test.
Apache::TestMM(3pm)	Provide MakeMaker Wrapper Methods.
Apache::TestReport(3pm)	A parent class for generating bug/success reports.
Apache::TestRequest(3pm)	Send requests to your Apache test server.
Apache::TestRun(3pm)	Run the test suite.
Apache::TestRunPerl(3pm)	Run mod_perl-requiring Test Suite.
Apache::TestRunPHP(3pm)	Configure and run a PHP-based test suite.
Apache::TestSmoke(3pm)	Special Tests Sequence Failure Finder.
Apache::TestTrace(3pm)	Helper output generation functions.
Apache::TestUtil(3pm)	Utility functions for writing tests.
Apache::TS(3pm)	…
Apache::TS::AdminClient(3pm)	…
Apache::TS::Config::Records(3pm)	Manage the Apache Traffic Server records.config file.
Apache::XMLRPC(3pm)	Serve XML-RPC requests from Apache.
Apache::XMLRPC::Lite(3pm)	Mod_perl-based XML-RPC server with minimum configuration.
App::Alice(3pm)	An Altogether Lovely Internet Chatting Experience.
App::AllKnowingDNS::Config(3pm)	Configuration object.
App::AllKnowingDNS::Handler(3pm)	Main code of AllKnowingDNS.
App::AllKnowingDNS::Util(3pm)	Utility functions.
App::Asciio(3pm)	Plain ASCII diagram.
App::Bot::BasicBot::Pluggable(3pm)	Base class for bot applications.
App::Bot::BasicBot::Pluggable::Terminal(3pm)	Alters the default bot class to Bot::BasicBot::Pluggable::Terminal.
App::Cache(3pm)	Easy application-level caching.
App::Cleo(3pm)	Play back shell commands for live demonstrations.
App::CLI(3pm)	Dispatcher module for command line interface programs.
App::CLI::Command(3pm)	Base class for App::CLI commands.
App::CLI::Command::Help(3pm)	Output PODs of each command.
App::ClusterSSH(3pm)	A container for functions of the ClusterSSH programs.
App::ClusterSSH::Base(3pm)	Base object provding utility functions.
App::ClusterSSH::Cluster(3pm)	Object representing cluster configuration.
App::ClusterSSH::Config(3pm)	Object representing application configuration.
App::ClusterSSH::Getopt(3pm)	Module to process command line args.
App::ClusterSSH::Helper(3pm)	Object representing helper script.
App::ClusterSSH::Host(3pm)	Object representing a host.
App::ClusterSSH::L10N(3pm)	Base translations module.
App::ClusterSSH::L10N::en(3pm)	Base English translations module.
App::Cmd(3pm)	Write command line apps with less suffering.
App::Cmd::ArgProcessor(3pm)	App::Cmd-specific wrapper for Getopt::Long::Descriptive.
App::Cmd::Command(3pm)	A base class for App::Cmd commands.
App::Cmd::Command::commands(3pm)	List the application's commands.
App::Cmd::Command::help(3pm)	Display a command's help screen.
App::Cmd::Command::version(3pm)	Display an app's version.
App::Cmd::Plugin(3pm)	A plugin for App::Cmd commands.
App::Cmd::Plugin::Prompt(3pm)	Plug prompting routines into your commands.
App::Cmd::Setup(3pm)	Helper for setting up App::Cmd classes.
App::Cmd::Simple(3pm)	A helper for building one-command App::Cmd applications.
App::Cmd::Subdispatch(3pm)	An App::Cmd::Command that is also an App::Cmd.
App::Cmd::Subdispatch::DashedStyle(3pm)	"app cmd --subcmd" style subdispatching.
App::Cmd::Tester(3pm)	For capturing the result of running an app.
App::Cmd::Tester::CaptureExternal(3pm)	Extends App::Cmd::Tester to capture from external subprograms.
App::Cmd::Tutorial(3pm)	Getting started with App::Cmd.
App::Cme(3pm)	Check or edit configuration data with Config::Model.
App::Cme::Command::check(3pm)	Check the configuration of an application.
App::Cme::Command::dump(3pm)	Dump the configuration of an application.
App::Cme::Command::edit(3pm)	Edit the configuration of an application.
App::Cme::Command::fix(3pm)	Fix the configuration of an application.
App::Cme::Command::fusefs(3pm)	Edit the configuration of an application with fuse.
App::Cme::Command::gen_class_pod(3pm)	Generates pod doc from model files.
App::Cme::Command::list(3pm)	List applications handled by cme.
App::Cme::Command::meta(3pm)	Edit the configuration of an application.
App::Cme::Command::migrate(3pm)	Migrate the configuration of an application.
App::Cme::Command::modify(3pm)	Modify the configuration of an application.
App::Cme::Command::search(3pm)	Search the configuration of an application.
App::Cme::Command::shell(3pm)	Edit the configuration of an application with a shell.
App::Cme::Command::update(3pm)	Update the configuration of an application.
App::Cme::Common(3pm)	Common methods for App::Cme.
App::Control(3pm)	Perl module for apachectl style control of another script or executable.
App::Control::Apache(3pm)	App::Control subclass for apache.
App::cpanlistchanges(3pm)	List changes for CPAN modules.
App::cpanminus(3pm)	Get, unpack, build and install modules from CPAN.
App::cpanminus::fatscript(3pm)	Get, unpack build and install modules from CPAN.
App::cpanoutdated(3pm)	Detect outdated CPAN modules in your environment.
App::CPANTS::Lint(3pm)	Front-end to Module::CPANTS::Analyse.
App::Daemon(3pm)	Start an Application as a Daemon.
App::FatPacker(3pm)	Pack your dependencies onto your script file.
App::FatPacker::Trace(3pm)	Tracing module usage using compilation checking.
App::Icli(3pm)	Icinga Command Line Interface.
App::Icli::ConfigData(3pm)	Configuration for App::Icli.
App::Info(3pm)	Information about software packages on a system.
App::Info::Handler(3pm)	App::Info event handler base class.
App::Info::Handler::Carp(3pm)	Use Carp to handle App::Info events.
App::Info::Handler::Print(3pm)	Print App::Info event messages.
App::Info::Handler::Prompt(3pm)	Prompting App::Info event handler.
App::Info::HTTPD(3pm)	Information about web servers on a system.
App::Info::HTTPD::Apache(3pm)	Information about Apache web server.
App::Info::Lib(3pm)	Information about software libraries on a system.
App::Info::Lib::Expat(3pm)	Information about the Expat XML parser.
App::Info::Lib::Iconv(3pm)	Information about libiconv.
App::Info::Lib::OSSPUUID(3pm)	Information about the OSSP UUID library.
App::Info::RDBMS(3pm)	Information about databases on a system.
App::Info::RDBMS::PostgreSQL(3pm)	Information about PostgreSQL.
App::Info::RDBMS::SQLite(3pm)	Information about SQLite.
App::Info::Request(3pm)	App::Info event handler request object.
App::Info::Util(3pm)	Utility class for App::Info subclasses.
App::KGB(3pm)	Collaborative IRC helper.
App::KGB::API(3pm)	…
App::KGB::Change(3pm)	A single file change.
App::KGB::Client(3pm)	Relay commits to KGB servers.
App::KGB::Client::CVS(3pm)	KGB interface to CVS.
App::KGB::Client::Fake(3pm)	Fake KGB client.
App::KGB::Client::Git(3pm)	Git support for KGB client.
App::KGB::Client::RelayMsg(3pm)	Simple message relay KGB client.
App::KGB::Client::ServerRef(3pm)	Server instance in KGB client.
App::KGB::Client::Subversion(3pm)	KGB interface to Subversion.
App::KGB::Commit(3pm)	A single commit.
App::KGB::Commit::Tag(3pm)	A helper class for describing tags.
App::KGB::Painter(3pm)	…
App::mkdist(3pm)	Create distributions that will use Module::Package::RDF.
App::Nopaste(3pm)	Easy access to any pastebin.
App::Nopaste::Command(3pm)	Command-line utility for App::Nopaste.
App::Nopaste::Service(3pm)	Base class for nopaste services.
App::Nopaste::Service::Codepeek(3pm)	(DEPRECATED) Service for Codepeek - http://codepeek.com.
App::Nopaste::Service::Debian(3pm)	Service provider for Debian - http://paste.debian.net/.
App::Nopaste::Service::Gist(3pm)	Service provider for GitHub gist - http://gist.github.com/.
App::Nopaste::Service::Mojopaste(3pm)	Service provider for mojopaste.
App::Nopaste::Service::PastebinCom(3pm)	Service provider for Pastebin - http://pastebin.com/.
App::Nopaste::Service::Pastie(3pm)	Service provider for Pastie - pastie.org.
App::Nopaste::Service::Shadowcat(3pm)	Service provider for Shadowcat - http://paste.scsys.co.uk/.
App::Nopaste::Service::Snitch(3pm)	Service provider for Snitch - http://nopaste.snit.ch/.
App::Nopaste::Service::ssh(3pm)	Copies files to your server using scp.
App::Nopaste::Service::Ubuntu(3pm)	Service provider for Ubuntu - http://paste.ubuntu.com/.
App::Options(3pm)	Combine command line options, environment vars, and option file values (for program.
App::Packer::PAR(3pm)	Pack applications in a single executable file.
App::Parcimonie(3pm)	Tools for the parcimonie program.
App::Parcimonie::Applet(3pm)	Systray applet object monitoring parcimonie's activities.
App::Parcimonie::Daemon(3pm)	Parcimonie daemon class.
App::Parcimonie::DBus::Object(3pm)	Provide parcimonie's D-Bus service and interface.
App::Parcimonie::GnuPG::Interface(3pm)	Parcimonie's GnuPG::Interface subclass.
App::Parcimonie::Role::HasCodeset(3pm)	Role to get the codeset being used.
App::Parcimonie::Role::HasEncoding(3pm)	Role to provide an Encode::Encoding objet for the codeset being used.
App::perlbrew(3pm)	Manage perl installations in your "$HOME".
App::perlrdf(3pm)	Perlrdf command line utils.
App::perlrdf::Command::Query(3pm)	SPARQL extension for App-perlrdf.
App::perlrdf::Command::Void(3pm)	Generate VoID descriptions on the command line.
App::pherkin(3pm)	Run Cucumber tests from the command line.
App::Pinto(3pm)	Command-line driver for Pinto.
App::Pinto::Command(3pm)	Base class for pinto commands.
App::Pinto::Command::add(3pm)	Add local archives to the repository.
App::Pinto::Command::clean(3pm)	Remove orphaned distribution archives.
App::Pinto::Command::copy(3pm)	Create a new stack by copying another.
App::Pinto::Command::default(3pm)	Mark the default stack.
App::Pinto::Command::delete(3pm)	Permanently remove an archive.
App::Pinto::Command::diff(3pm)	Show difference between two stacks.
App::Pinto::Command::help(3pm)	Display a command's help screen.
App::Pinto::Command::init(3pm)	Create a new repository.
App::Pinto::Command::install(3pm)	Install stuff from the repository.
App::Pinto::Command::kill(3pm)	Permanently delete a stack.
App::Pinto::Command::list(3pm)	Show the packages in a stack.
App::Pinto::Command::lock(3pm)	Mark a stack as read-only.
App::Pinto::Command::log(3pm)	Show the revision logs of a stack.
App::Pinto::Command::manual(3pm)	Show the full manual for a command.
App::Pinto::Command::migrate(3pm)	Migrate repository to a new version.
App::Pinto::Command::new(3pm)	Create a new empty stack.
App::Pinto::Command::nop(3pm)	Do nothing.
App::Pinto::Command::pin(3pm)	Force a package to stay in a stack.
App::Pinto::Command::props(3pm)	Show or set stack properties.
App::Pinto::Command::pull(3pm)	Pull archives from upstream repositories.
App::Pinto::Command::register(3pm)	Put existing packages on a stack.
App::Pinto::Command::rename(3pm)	Change the name of a stack.
App::Pinto::Command::roots(3pm)	Show the roots of a stack.
App::Pinto::Command::stacks(3pm)	Show available stacks.
App::Pinto::Command::statistics(3pm)	Report statistics about the repository.
App::Pinto::Command::thanks(3pm)	Show some gratitude.
App::Pinto::Command::unlock(3pm)	Mark a stack as writable.
App::Pinto::Command::unpin(3pm)	Free packages that have been pinned.
App::Pinto::Command::unregister(3pm)	Remove packages from a stack.
App::Pinto::Command::verify(3pm)	Report archives that are missing.
App::pmuninstall(3pm)	Uninstall modules.
App::Prolix(3pm)	Trim chatty command outputs.
App::Prolix::MooseHelpers(3pm)	Moose helpers for App::Prolix.
App::Prove(3pm)	Implements the "prove" command.
App::Prove::Plugin::HTML(3pm)	A prove plugin for HTML output.
App::Prove::State(3pm)	State storage for the "prove" command.
App::Prove::State::Result(3pm)	Individual test suite results.
App::Prove::State::Result::Test(3pm)	Individual test results.
App::PRT(3pm)	Command line Perl Refactoring Tool.
App::Rad(3pm)	Rapid (and easy!) creation of command line applications.
App::Rad::Exclude(3pm)	'exclude' command extension for App::Rad.
App::Rad::Help(3pm)	'help' command extension for App::Rad.
App::Rad::Include(3pm)	'include' command extension for App::Rad.
App::Rad::Plugin(3pm)	Extend the App::Rad framework!.
App::rdfns(3pm)	Quickly get common URI namespaces.
App::REPL(3pm)	A container for functions for the iperl program.
App::SD(3pm)	A distributed ticket tracking system.
App::SD::CLI::Command(3pm)	…
App::SD::CLI::Model::Ticket(3pm)	…
App::SD::ForeignReplica(3pm)	…
App::SD::ForeignReplica::PullEncoder(3pm)	…
App::SD::Model::Ticket(3pm)	…
App::SD::Replica::debbugs(3pm)	…
App::SD::Replica::debbugs::PullEncoder(3pm)	…
App::SD::Replica::debbugs::PushEncoder(3pm)	…
App::SD::Replica::gcode::PullEncoder(3pm)	…
App::SD::Replica::github(3pm)	…
App::SD::Replica::github::PullEncoder(3pm)	…
App::SD::Replica::hm(3pm)	…
App::SD::Replica::lighthouse::PullEncoder(3pm)	…
App::SD::Replica::rt(3pm)	…
App::SD::Replica::rt::PullEncoder(3pm)	…
App::SD::Replica::trac(3pm)	…
App::SD::Replica::trac::PullEncoder(3pm)	…
App::SD::Server(3pm)	…
App::SD::Test(3pm)	…
App::SD::Util(3pm)	…
App::Sqitch(3pm)	…
App::Sqitch::Command(3pm)	…
App::Sqitch::Command::add(3pm)	…
App::Sqitch::Command::bundle(3pm)	…
App::Sqitch::Command::checkout(3pm)	…
App::Sqitch::Command::config(3pm)	…
App::Sqitch::Command::deploy(3pm)	…
App::Sqitch::Command::engine(3pm)	…
App::Sqitch::Command::help(3pm)	…
App::Sqitch::Command::init(3pm)	…
App::Sqitch::Command::log(3pm)	…
App::Sqitch::Command::plan(3pm)	…
App::Sqitch::Command::rebase(3pm)	…
App::Sqitch::Command::revert(3pm)	…
App::Sqitch::Command::rework(3pm)	…
App::Sqitch::Command::show(3pm)	…
App::Sqitch::Command::status(3pm)	…
App::Sqitch::Command::tag(3pm)	…
App::Sqitch::Command::target(3pm)	…
App::Sqitch::Command::upgrade(3pm)	…
App::Sqitch::Command::verify(3pm)	…
App::Sqitch::Config(3pm)	…
App::Sqitch::DateTime(3pm)	…
App::Sqitch::Engine(3pm)	…
App::Sqitch::Engine::firebird(3pm)	…
App::Sqitch::Engine::mysql(3pm)	…
App::Sqitch::Engine::oracle(3pm)	…
App::Sqitch::Engine::pg(3pm)	…
App::Sqitch::Engine::sqlite(3pm)	…
App::Sqitch::Engine::vertica(3pm)	…
App::Sqitch::ItemFormatter(3pm)	…
App::Sqitch::Plan(3pm)	…
App::Sqitch::Plan::Blank(3pm)	…
App::Sqitch::Plan::Change(3pm)	…
App::Sqitch::Plan::ChangeList(3pm)	…
App::Sqitch::Plan::Depend(3pm)	…
App::Sqitch::Plan::Line(3pm)	…
App::Sqitch::Plan::LineList(3pm)	…
App::Sqitch::Plan::Pragma(3pm)	…
App::Sqitch::Plan::Tag(3pm)	…
App::Sqitch::Role::DBIEngine(3pm)	…
App::Sqitch::Role::RevertDeployCommand(3pm)	…
App::Sqitch::Role::TargetConfigCommand(3pm)	…
App::Sqitch::Target(3pm)	…
App::Sqitch::Types(3pm)	…
App::Sqitch::X(3pm)	…
App::Stacktrace(3pm)	Stack trace.
App::Termcast(3pm)	Broadcast your terminal sessions for remote viewing.
App::Whiff(3pm)	Find the first executable of a series of alternatives.
AppConfig(3pm)	Perl5 module for reading configuration files and parsing command line arguments.
AppConfig::Args(3pm)	Perl5 module for reading command line arguments.
AppConfig::CGI(3pm)	Perl5 module for processing CGI script parameters.
AppConfig::File(3pm)	Perl5 module for reading configuration files.
AppConfig::Getopt(3pm)	Perl5 module for processing command line arguments via delegation to Getopt::Long.
AppConfig::State(3pm)	Application configuration state.
AppConfig::Std(3pm)	Subclass of AppConfig that provides standard options.
AppConfig::Sys(3pm)	Perl5 module defining platform-specific information and methods for other AppConfig::*.
appendpdf(1p)	Append one PDF to another.
Application.pm(3)	AAT Application module.
apply_diff_relay_logs(1p)	Generating differential relay logs between the latest slave and target slave, and.
applypatch(1p)	Apply 'makepatch' generated script to update a source tree.
APR(3pm)	Perl Interface for Apache Portable Runtime (libapr and libaprutil Libraries).
APR::Base64(3pm)	Perl API for APR base64 encoding/decoding functionality.
APR::Brigade(3pm)	Perl API for manipulating APR Bucket Brigades.
APR::Bucket(3pm)	Perl API for manipulating APR Buckets.
APR::BucketAlloc(3pm)	Perl API for Bucket Allocation.
APR::BucketType(3pm)	Perl API for APR bucket types.
APR::Const(3pm)	Perl Interface for APR Constants.
APR::Date(3pm)	Perl API for APR date manipulating functions.
APR::Error(3pm)	Perl API for APR/Apache/mod_perl exceptions.
APR::Finfo(3pm)	Perl API for APR fileinfo structure.
APR::IpSubnet(3pm)	Perl API for accessing APRs ip_subnet structures.
APR::OS(3pm)	Perl API for Platform-specific APR API.
APR::PerlIO(3pm)	…
APR::Pool(3pm)	Perl API for APR pools.
APR::Request(3pm)	Wrapper for libapreq2's module/handle API.
APR::Request::Apache2(3pm)	Wrapper for a mod_apreq2 handle.
APR::Request::CGI(3pm)	Wrapper for libapreq2's CGI handle.
APR::Request::Cookie(3pm)	Wrapper for libapreq2's cookie API.
APR::Request::Error(3pm)	Wrapper for libapreq2's error API.
APR::Request::Hook(3pm)	Wrapper for libapreq2's hook API.
APR::Request::Param(3pm)	Wrapper for libapreq2's param API.
APR::Request::Parser(3pm)	Wrapper for libapreq2's parser API.
APR::SockAddr(3pm)	Perl API for APR socket address structure.
APR::Socket(3pm)	Perl API for APR sockets.
APR::Status(3pm)	Perl Interface to the APR_STATUS_IS_* macros.
APR::String(3pm)	Perl API for manipulating APR UUIDs.
APR::Table(3pm)	Perl API for manipulating APR opaque string-content tables.
APR::ThreadMutex(3pm)	Perl API for APR thread mutexes.
APR::ThreadRWLock(3pm)	Perl API for APR thread read/write locks.
APR::URI(3pm)	Perl API for URI manipulations.
APR::Util(3pm)	Perl API for Various APR Utilities.
APR::UUID(3pm)	Perl API for manipulating APR UUIDs.
apt-mirror(1)	Apt sources mirroring tool.
apt-show-source(1p)	Lists source-packages.
apt-show-versions(1p)	Lists available package versions with distribution.
apt-src(1p)	Manage debian source package trees.
AptPkg(3pm)	Interface to libapt-pkg.
AptPkg::Cache(3pm)	APT package cache interface.
AptPkg::Config(3pm)	APT configuration interface.
AptPkg::hash(3pm)	A helper class for implementing tied hashes.
AptPkg::PkgRecords(3pm)	APT package description class.
AptPkg::Policy(3pm)	APT package version policy class.
AptPkg::Source(3pm)	APT source package interface.
AptPkg::System(3pm)	APT system abstraction class.
AptPkg::Version(3pm)	APT package versioning class.
Arch(3pm)	GNU Arch Perl library.
Arch::Backend(3pm)	Arch backend feature specific functions.
Arch::Changes(3pm)	Class representing a list of changes.
Arch::Changeset(3pm)	Class representing Arch changeset.
Arch::DiffParser(3pm)	Parse file's diff and perform some manipulations.
Arch::FileHighlighter(3pm)	Syntax-highlight file's content using markup.
Arch::Inventory(3pm)	Class representing a tree inventory.
Arch::Library(3pm)	Access arch revision libraries.
Arch::LiteWeb(3pm)	Simple way to access web pages.
Arch::Log(3pm)	Class representing Arch patch-log.
Arch::Name(3pm)	Parse, store and construct an arch name.
Arch::Registry(3pm)	Manage registered archives, search archives on the web.
Arch::RevisionBunches(3pm)	Manage bunches of related revisions.
Arch::Run(3pm)	Run subprocesses and capture output.
Arch::RunLimit(3pm)	Class to enforce a limit on the number of running processes.
Arch::Session(3pm)	Access arch archives.
Arch::SharedCache(3pm)	A synchronized data structure (map) for IPC.
Arch::SharedIndex(3pm)	A synchronized data structure (map) for IPC.
Arch::Storage(3pm)	Abstract class to access arch archives.
Arch::Tarball(3pm)	An interface to create and work with tarballs.
Arch::TempFiles(3pm)	Help to manage temporary files/dirs.
Arch::Test::Archive(3pm)	A test framework for Arch-Perl.
Arch::Test::Cases(3pm)	A test framework for Arch-Perl.
Arch::Test::Framework(3pm)	A test framework for Arch-Perl.
Arch::Test::Tree(3pm)	A test framework for Arch-Perl.
Arch::Tree(3pm)	Class representing Arch tree.
Arch::Util(3pm)	Arch utility functions.
Archive::Any(3pm)	Single interface to deal with file archives.
Archive::Any::Create(3pm)	Abstract API to create archives (tar.gz and zip).
Archive::Any::Lite(3pm)	Simple CPAN package extractor.
Archive::Any::Plugin(3pm)	Anatomy of an Archive::Any plugin.
Archive::Any::Plugin::Tar(3pm)	Archive::Any wrapper around Archive::Tar.
Archive::Any::Plugin::Zip(3pm)	Archive::Any wrapper around Archive::Zip.
Archive::Any::Tar(3pm)	Archive::Any wrapper around Archive::Tar.
Archive::Any::Zip(3pm)	Archive::Any wrapper around Archive::Zip.
Archive::Ar(3pm)	Interface for manipulating ar archives.
Archive::Extract(3pm)	A generic archive extracting mechanism.
Archive::Peek(3pm)	Peek into archives without extracting them.
Archive::Tar::Wrapper(3pm)	API wrapper around the 'tar' utility.
Archive::Zip(3pm)	Provide an interface to ZIP archive files.
Archive::Zip::FAQ(3pm)	Answers to a few frequently asked questions about Archive::Zip.
Archive::Zip::MemberRead(3pm)	A wrapper that lets you read Zip archive members as if they were files.
Archive::Zip::Tree(3pm)	(DEPRECATED) methods for adding/extracting trees using Archive::Zip.
arename(1)	Automatically rename audio files by tagging information.
ArinWhois(3pm)	Perl extension to retrieve information from ARIN Whois database.
Array(3pm)	Perl Array handling and conversion between Perl arrays and C array pointers.
Array::Compare(3pm)	Perl extension for comparing arrays.
Array::Diff(3pm)	Find the differences between two arrays.
Array::Group(3pm)	Convert an array into array of arrayrefs of uniform size N.
Array::IntSpan(3pm)	Handles arrays of scalars or objects using integer ranges.
Array::IntSpan::Fields(3pm)	IntSpan array using integer fields as indices.
Array::IntSpan::IP(3pm)	A Module for arrays using IP addresses as indices.
Array::Iterator(3pm)	A simple class for iterating over Perl arrays.
Array::Iterator::BiDirectional(3pm)	A subclass of Array::Iterator to allow forwards and backwards iteration.
Array::Iterator::Circular(3pm)	A subclass of Array::Iterator to allow circular iteration.
Array::Iterator::Reusable(3pm)	A subclass of Array::Iterator to allow reuse of iterators.
Array::PrintCols(3pm)	Print or format array elements in vertically sorted columns.
Array::RefElem(3pm)	Set up array elements as aliases.
Array::Unique(3pm)	Tie-able array that allows only unique values.
Array::Utils(3pm)	Small utils for array manipulation.
artemis(1)	Interactive EXAFS data analysis.
asa(3pm)	Lets your class/object say it works like something else.
asp-perl(1p)	Apache::ASP CGI and command line script processor.
Aspect(3pm)	Aspect-Oriented Programming (AOP) for Perl.
Aspect::Advice(3pm)	Change how Perl code is run at a pointcut.
Aspect::Advice::After(3pm)	Execute code after a function is called.
Aspect::Advice::Around(3pm)	Execute code both before and after a function.
Aspect::Advice::Before(3pm)	Execute code before a function is called.
Aspect::Guard(3pm)	General purpose guard object for destroy-time actions.
Aspect::Hook(3pm)	Holding area for internal generated code.
Aspect::Legacy(3pm)	Legacy Compatibility for Aspect.pm.
Aspect::Library(3pm)	Base class for all reusable aspects.
Aspect::Library::Breakpoint(3pm)	A breakpoint aspect.
Aspect::Library::Listenable(3pm)	Observer pattern with events.
Aspect::Library::Singleton(3pm)	A singleton aspect.
Aspect::Library::Wormhole(3pm)	A wormhole between call frames.
Aspect::Modular(3pm)	First generation base class for reusable aspects.
Aspect::Point(3pm)	The Join Point context.
Aspect::Point::Functions(3pm)	Allow point context methods to be called as functions.
Aspect::Point::Static(3pm)	The Join Point context for join point static parts.
Aspect::Pointcut(3pm)	API for determining which events should be hooked.
Aspect::Pointcut::And(3pm)	Logical 'and' pointcut.
Aspect::Pointcut::Call(3pm)	Call pointcut.
Aspect::Pointcut::Cflow(3pm)	Cflow pointcut.
Aspect::Pointcut::Highest(3pm)	Pointcut for preventing recursive matching.
Aspect::Pointcut::Logic(3pm)	Pointcut logic role.
Aspect::Pointcut::Not(3pm)	Logical 'not' pointcut.
Aspect::Pointcut::Or(3pm)	Logical 'or' pointcut.
Aspect::Pointcut::Returning(3pm)	Function returning without exception.
Aspect::Pointcut::Throwing(3pm)	Exception typing pointcut.
Aspect::Pointcut::True(3pm)	Pointcut that allows arbitrary Perl code.
Aspect::Pointcut::Wantarray(3pm)	A pointcut for the run-time wantarray context.
Asterisk::AGI(3pm)	Simple Asterisk Gateway Interface Class.
Asterisk::Manager(3pm)	Asterisk Manager Interface.
Asterisk::Outgoing(3pm)	Create outgoing call queue file.
Asterisk::Voicemail(3pm)	Stuff to deal with asterisk voicemail.
Astro::FITS::CFITSIO(3pm)	Perl extension for using the cfitsio library.
Astro::FITS::Header(3pm)	Object Orientated interface to FITS HDUs.
Astro::FITS::Header::AST(3pm)	Manipulates FITS headers from an AST object.
Astro::FITS::Header::CFITSIO(3pm)	Manipulates FITS headers from a FITS file.
Astro::FITS::Header::GSD(3pm)	Manipulate FITS headers from GSD files.
Astro::FITS::Header::Item(3pm)	A card image from a FITS header.
Astro::FITS::Header::NDF(3pm)	Manipulate FITS headers from NDF files.
asused(3pm)	Summaries address space used and according to the RIPE DB and REG.
Async::Interrupt(3pm)	Allow C/XS libraries to interrupt perl asynchronously.
Async::MergePoint(3pm)	Resynchronise diverged control flow.
ataglist(1)	Print audio file metadata.
atitvout(1)	ATI Rage/Radeon TV Out configuration program.
AtomBus(3pm)	An AtomPub server for messaging.
AtomBus::Schema(3pm)	…
AtomBus::Schema::Result::AtomBusEntry(3pm)	…
AtomBus::Schema::Result::AtomBusFeed(3pm)	…
Atompub(3pm)	Atom Publishing Protocol implementation.
Atompub::Client(3pm)	A client for the Atom Publishing Protocol.
Atompub::DateTime(3pm)	A date and time object for the Atom Publishing Protocol.
Atompub::MediaType(3pm)	A media type object for the Atom Publishing Protocol.
Atompub::Server(3pm)	A server for the Atom Publishing Protocol.
Atompub::Util(3pm)	Utility functions.
atoms(1p)	Make lists of atomic coordinates from crystallographic data.
Attean(3pm)	A Semantic Web Framework.
Attean::AggregateExpression(3pm)	Representation of aggregate expression trees.
Attean::Algebra(3pm)	Representation of SPARQL algebra operators.
Attean::API(3pm)	Utility package for loading all Attean role packages.
Attean::API::AbbreviatingParser(3pm)	Role for parsers that use construct absolute IRIs based on prefixed names or.
Attean::API::AbbreviatingSerializer(3pm)	Role for serializers that can abbreviate IRIs as prefixed names or.
Attean::API::AggregateExpression(3pm)	Role representing an aggregate expression tree.
Attean::API::AppendableSerializer(3pm)	Role for serializers that can be repeatedly invoked while keeping output.
Attean::API::AtOnceParser(3pm)	Role for parsers that natively parse all input before returning any data.
Attean::API::Binding(3pm)	Name to term bindings.
Attean::API::Blank(3pm)	Role representing RDF blank terms.
Attean::API::BlankOrIRI(3pm)	Role representing blank or IRI terms.
Attean::API::BulkUpdatableModel(3pm)	Role representing models that can perform bulk update operations.
Attean::API::Expression(3pm)	SPARQL expressions.
Attean::API::IRI(3pm)	Role representing RDF IRI terms.
Attean::API::Iterator(3pm)	Typed iterator.
Attean::API::Literal(3pm)	Role representing RDF Literal terms.
Attean::API::MixedStatementParser(3pm)	Role for parsers of Attean::API::TripleOrQuad objects.
Attean::API::MixedStatementSerializer(3pm)	Role for serializers of Attean::API::TripleOrQuad objects.
Attean::API::Model(3pm)	RDF Model.
Attean::API::MutableModel(3pm)	Role representing mutable models.
Attean::API::MutableTripleStore(3pm)	Role representing mutable triple stores.
Attean::API::Parser(3pm)	Parser role.
Attean::API::Plan(3pm)	Query plan.
Attean::API::PullParser(3pm)	Role for parsers that natively return an iterator.
Attean::API::PushParser(3pm)	Role for parsers that natively call a callback function for each parsed item.
Attean::API::Quad(3pm)	Role representing quads.
Attean::API::QuadParser(3pm)	Role for parsers of Attean::API::Quad objects.
Attean::API::QuadPattern(3pm)	Role representing quad patterns.
Attean::API::QuadSerializer(3pm)	Role for serializers of Attean::API::Quad objects.
Attean::API::Query(3pm)	Utility package defining query-related roles.
Attean::API::QueryPlanner(3pm)	Iterative dynamic programming query planning role.
Attean::API::RepeatableIterator(3pm)	Role representing iterators that may be reset and iterated again.
Attean::API::Result(3pm)	Role representing a set of variable bindings.
Attean::API::ResultParser(3pm)	Role for parsers of Attean::API::Result objects.
Attean::API::ResultSerializer(3pm)	Role for serializers of Attean::API::Result objects.
Attean::API::Serializer(3pm)	Serializer role.
Attean::API::Store(3pm)	Triple/quad store role.
Attean::API::Term(3pm)	RDF Terms.
Attean::API::TermOrVariable(3pm)	Role representing terms and variables.
Attean::API::TermParser(3pm)	Role for parsers of Attean::API::Term objects.
Attean::API::TermSerializer(3pm)	Role for serializers of Attean::API::Term objects.
Attean::API::Triple(3pm)	Role representing triples.
Attean::API::TripleOrQuad(3pm)	Role representing triples and quads.
Attean::API::TripleParser(3pm)	Role for parsers of Attean::API::Triple objects.
Attean::API::TriplePattern(3pm)	Role representing triple patterns.
Attean::API::TripleSerializer(3pm)	Role for serializers of Attean::API::Triple objects.
Attean::API::Variable(3pm)	Role representing term variables.
Attean::BindingEqualityTest(3pm)	Test for equality of binding sets with bnode isomorphism.
Attean::Blank(3pm)	RDF blank nodes.
Attean::CodeIterator(3pm)	Iterator implementation backed by a generator function.
Attean::Expression(3pm)	SPARQL Expressions.
Attean::IDPQueryPlanner(3pm)	Iterative dynamic programming query planner.
Attean::IRI(3pm)	RDF Internationalized Resource Identifiers (IRIs).
Attean::IteratorSequence(3pm)	Iterator implementation backed by zero or more sub-iterators.
Attean::ListIterator(3pm)	Iterator implementation backed by a list/array of values.
Attean::Literal(3pm)	RDF Literals.
Attean::Plan(3pm)	Representation of SPARQL query plan operators.
Attean::Quad(3pm)	RDF Quads.
Attean::QuadModel(3pm)	RDF model backed by a quad-store.
Attean::QueryPlanner(3pm)	Query planner.
Attean::RDF(3pm)	Utility package for exporting shorthand functions for constructing RDF objects.
Attean::Result(3pm)	SPARQL Result.
Attean::SimpleQueryEvaluator(3pm)	Simple query evaluator.
Attean::TermMap(3pm)	Mapping terms to new terms.
Attean::TreeRewriter(3pm)	Walk and rewrite subtrees.
Attean::Triple(3pm)	RDF Triples.
Attean::TripleModel(3pm)	RDF model backed by a set of triple-stores.
Attean::Variable(3pm)	Pattern matching variables.
AtteanX::API::JoinRotatingPlanner(3pm)	Query planning role to produce alternative join plans.
AtteanX::API::Lexer(3pm)	Role defining common functionality for lexers.
AtteanX::Model::SPARQL(3pm)	Attean SPARQL Model.
AtteanX::Parser::NQuads(3pm)	N-Quads Parser.
AtteanX::Parser::NTriples(3pm)	N-Triples Parser.
AtteanX::Parser::NTuples(3pm)	Shared functionality for N-Triples and N-Quads parsers.
AtteanX::Parser::RDFXML(3pm)	RDF/XML Parser.
AtteanX::Parser::SPARQL(3pm)	SPARQL 1.1 Parser.
AtteanX::Parser::SPARQLJSON(3pm)	SPARQL JSON Parser.
AtteanX::Parser::SPARQLLex(3pm)	SPARQL Lexer.
AtteanX::Parser::SPARQLTSV(3pm)	SPARQL Results TSV Parser.
AtteanX::Parser::SPARQLXML(3pm)	SPARQL XML Parser.
AtteanX::Parser::SPARQLXML::SAXHandler(3pm)	XML parser for SPARQL XML Results format.
AtteanX::Parser::Turtle(3pm)	Turtle RDF Parser.
AtteanX::Parser::Turtle::Constants(3pm)	Constant definitions for use in parsing Turtle, TriG, and N-Triples.
AtteanX::Parser::Turtle::Lexer(3pm)	Tokenizer for parsing Turtle, TriG, and N-Triples.
AtteanX::Parser::Turtle::Token(3pm)	Token objects used for parsing of Turtle.
AtteanX::RDFQueryTranslator(3pm)	Translate RDF::Query objects to Attean::API::Algebra objects.
AtteanX::Serializer::CanonicalNTriples(3pm)	Canonical N-Triples Serializer.
AtteanX::Serializer::NQuads(3pm)	N-Triples Serializer.
AtteanX::Serializer::NTriples(3pm)	N-Triples Serializer.
AtteanX::Serializer::NTuples(3pm)	Shared functionality for N-Triples and N-Quads serializers.
AtteanX::Serializer::SPARQL(3pm)	SPARQL Serializer.
AtteanX::Serializer::SPARQLCSV(3pm)	SPARQL Results CSV Serializer.
AtteanX::Serializer::SPARQLHTML(3pm)	SPARQL Results HTML Serializer.
AtteanX::Serializer::SPARQLTSV(3pm)	SPARQL Results TSV Serializer.
AtteanX::Serializer::SPARQLXML(3pm)	SPARQL Results XML Serializer.
AtteanX::Serializer::Turtle(3pm)	Turtle Serializer.
AtteanX::Serializer::TurtleTokens(3pm)	Turtle Serializer.
AtteanX::SPARQL::Constants(3pm)	Constant definitions for use in parsing and serializing SPARQL.
AtteanX::SPARQL::Token(3pm)	Token objects used for parsing and serializing SPARQL.
AtteanX::Store::Memory(3pm)	Simple in-memory RDF store.
AtteanX::Store::README(3pm)	Attean SPARQL store.
AtteanX::Store::Simple(3pm)	Simple, unindexed, in-memory RDF store.
AtteanX::Store::SimpleTripleStore(3pm)	SimpleTripleStore, unindexed, in-memory RDF store.
AtteanX::Store::SPARQL(3pm)	Attean SPARQL store.
AtteanX::Store::SPARQL::Plan::BGP(3pm)	Plan for efficient evaluation of SPARQL BGPs on remote endpoints.
Audio::APE(3pm)	An object-oriented interface to Monkey's Audio file information and APE tag fields.
Audio::CD(3pm)	Perl interface to libcdaudio (cd + cddb).
Audio::Ecasound(3pm)	Perl binding to the ecasound sampler, recorder, fx-processor.
Audio::File(3pm)	Audio file abstraction library.
Audio::File::AudioProperties(3pm)	Abstract an audio files audio properties.
Audio::File::Tag(3pm)	Abstracts the tag of an audio file.
Audio::File::Type(3pm)	Represents an audio filetype.
Audio::FLAC::Decoder(3pm)	An object-oriented FLAC decoder.
Audio::FLAC::Header(3pm)	Interface to FLAC header metadata.
Audio::Mixer(3pm)	Perl extension for Sound Mixer control.
Audio::Moosic(3pm)	Moosic client library for Perl.
Audio::MPD(3pm)	Class to talk to MPD (Music Player Daemon) servers.
Audio::MPD::Collection(3pm)	Class to query MPD's collection.
Audio::MPD::Common(3pm)	Common helper classes for mpd.
Audio::MPD::Common::Item(3pm)	A generic collection item.
Audio::MPD::Common::Item::Directory(3pm)	A directory object.
Audio::MPD::Common::Item::Playlist(3pm)	A playlist object.
Audio::MPD::Common::Item::Song(3pm)	A song object with some audio tags.
Audio::MPD::Common::Output(3pm)	Class representing MPD output.
Audio::MPD::Common::Stats(3pm)	Class representing MPD stats.
Audio::MPD::Common::Status(3pm)	Class representing MPD status.
Audio::MPD::Common::Time(3pm)	Class representing time of current song.
Audio::MPD::Common::Types(3pm)	Types used in the distribution.
Audio::MPD::Playlist(3pm)	Class to mess MPD's playlist.
Audio::MPD::Types(3pm)	Types used in the distribution.
Audio::Musepack(3pm)	An object-oriented interface to Musepack file information and APE tag fields.
Audio::Nama::ChainSetup(3pm)	Routines for generating Ecasound chain setup.
Audio::Nama::Globals(3pm)	Nama global variables.
Audio::Nama::Object(3pm)	Class builder.
Audio::RPLD(3pm)	Module to communicate with RoarAudio PlayList Daemon.
Audio::Scan(3pm)	Fast C metadata and tag reader for all common audio file formats.
Audio::Scrobbler(3pm)	Perl interface to audioscrobbler.com/last.fm.
Audio::Wav(3pm)	Modules for reading & writing Microsoft WAV files.
Audio::Wav::Read(3pm)	Module for reading Microsoft WAV files.
Audio::Wav::Write(3pm)	Module for writing Microsoft WAV files.
Audio::WMA(3pm)	Perl extension for reading WMA/ASF Metadata.
audio_rename(1p)	Rename an audio file via information got via MP3::Tag.
audiolink(1)	Create AudioLink config file, databases and tables.
Auth::Yubikey_Decrypter(3pm)	Decrypting the output from the yubikey token.
Auth::Yubikey_WebClient(3pm)	Authenticating the Yubikey against the Yubico Web API.
AuthCAS(3pm)	Client library for CAS 2.0 authentication server.
Authen::Bitcard(3pm)	Bitcard authentication verification.
Authen::Captcha(3pm)	Perl extension for creating captcha's to verify the human element in transactions.
Authen::CAS::Client(3pm)	Provides an easy-to-use interface for authentication using JA-SIG's Central.
Authen::CAS::Client::Response(3pm)	A set of classes for implementing responses from a CAS server.
Authen::DecHpwd(3pm)	DEC VMS password hashing.
Authen::Htpasswd(3pm)	Interface to read and modify Apache .htpasswd files.
Authen::Htpasswd::User(3pm)	Represents a user line in a .htpasswd file.
Authen::Htpasswd::Util(3pm)	Performs encryption of supported .htpasswd formats.
Authen::Krb5(3pm)	Perl extension for Kerberos 5.
Authen::Krb5::Admin(3pm)	Perl extension for MIT Kerberos 5 admin interface.
Authen::Krb5::Simple(3pm)	Basic user authentication using Kerberos 5.
Authen::NTLM(3pm)	An NTLM authentication module.
Authen::OATH(3pm)	OATH One Time Passwords.
Authen::PAM(3pm)	Perl interface to PAM library.
Authen::PAM::FAQ(3pm)	Frequently-Asked Questions about Authen::PAM.
Authen::Passphrase(3pm)	Hashed passwords/passphrases as objects.
Authen::Passphrase::AcceptAll(3pm)	Accept any passphrase.
Authen::Passphrase::BigCrypt(3pm)	Passphrases using bigcrypt algorithm.
Authen::Passphrase::BlowfishCrypt(3pm)	Passphrases using the Blowfish-based Unix crypt().
Authen::Passphrase::Clear(3pm)	Cleartext passphrases.
Authen::Passphrase::Crypt16(3pm)	Passphrases using Ultrix crypt16 algorithm.
Authen::Passphrase::DESCrypt(3pm)	Passphrases using the DES-based Unix crypt().
Authen::Passphrase::EggdropBlowfish(3pm)	Passphrases using Eggdrop's blowfish.mod.
Authen::Passphrase::LANManager(3pm)	Passphrases using the LAN Manager hash algorithm.
Authen::Passphrase::LANManagerHalf(3pm)	Passphrases using half the LAN Manager algorithm.
Authen::Passphrase::MD5Crypt(3pm)	Passphrases using the MD5-based Unix crypt().
Authen::Passphrase::MySQL323(3pm)	Passphrases using the MySQL v3.23 algorithm.
Authen::Passphrase::MySQL41(3pm)	Passphrases using the MySQL v4.1 algorithm.
Authen::Passphrase::NetscapeMail(3pm)	Passphrases using Netscape Mail Server's method.
Authen::Passphrase::NTHash(3pm)	Passphrases using the NT-Hash algorithm.
Authen::Passphrase::PHPass(3pm)	Passphrases using the phpass algorithm.
Authen::Passphrase::RejectAll(3pm)	Reject all passphrases.
Authen::Passphrase::SaltedDigest(3pm)	Passphrases using the generic salted digest algorithm.
Authen::Passphrase::VMSPurdy(3pm)	Passphrases with the VMS Purdy polynomial system.
Authen::Radius(3pm)	Provide simple Radius client facilities.
Authen::SASL(3pm)	SASL Authentication framework.
Authen::SASL::Cyrus(3pm)	XS code to glue Perl SASL to Cyrus SASL.
Authen::SASL::Perl(3pm)	…
Authen::SASL::Perl::ANONYMOUS(3pm)	Anonymous Authentication class.
Authen::SASL::Perl::CRAM_MD5(3pm)	CRAM MD5 Authentication class.
Authen::SASL::Perl::DIGEST_MD5(3pm)	Digest MD5 Authentication class.
Authen::SASL::Perl::EXTERNAL(3pm)	External Authentication class.
Authen::SASL::Perl::GSSAPI(3pm)	GSSAPI (Kerberosv5) Authentication class.
Authen::SASL::Perl::LOGIN(3pm)	Login Authentication class.
Authen::SASL::Perl::PLAIN(3pm)	Plain Login Authentication class.
Authen::SASL::SASLprep(3pm)	A Stringprep Profile for User Names and Passwords (RFC 4013).
Authen::SCRAM(3pm)	Salted Challenge Response Authentication Mechanism (RFC 5802).
Authen::SCRAM::Client(3pm)	RFC 5802 SCRAM client.
Authen::SCRAM::Server(3pm)	RFC 5802 SCRAM Server.
Authen::Simple(3pm)	Simple Authentication.
Authen::Simple::ActiveDirectory(3pm)	Simple ActiveDirectory authentication.
Authen::Simple::Adapter(3pm)	Adapter class for implementations.
Authen::Simple::Apache(3pm)	PerlAuthenHandler handler for Apache.
Authen::Simple::CDBI(3pm)	Simple Class::DBI authentication.
Authen::Simple::DBI(3pm)	Simple DBI authentication.
Authen::Simple::DBM(3pm)	Simple DBM authentication.
Authen::Simple::FTP(3pm)	Simple FTP authentication.
Authen::Simple::HTTP(3pm)	Simple HTTP authentication.
Authen::Simple::Kerberos(3pm)	Simple Kerberos authentication.
Authen::Simple::LDAP(3pm)	Simple LDAP authentication.
Authen::Simple::Log(3pm)	Simple log class.
Authen::Simple::PAM(3pm)	Simple PAM authentication.
Authen::Simple::Passwd(3pm)	Simple Passwd authentication.
Authen::Simple::Password(3pm)	Simple password checking.
Authen::Simple::POP3(3pm)	Simple POP3 authentication.
Authen::Simple::RADIUS(3pm)	Simple RADIUS authentication.
Authen::Simple::SMB(3pm)	Simple SMB authentication.
Authen::Simple::SMTP(3pm)	Simple SMTP authentication.
Authen::Smb(3pm)	Perl extension to authenticate against an SMB server.
Authen::TacacsPlus(3pm)	Perl extension for authentication using tacacs+ server.
autobox(3pm)	Call methods on native types.
autobox::Core(3pm)	Provide core functions to autoboxed scalars, arrays and hashes.
autobox::dump(3pm)	Human/perl readable strings from the results of an EXPR.
autobox::Junctions(3pm)	Autoboxified junction-style operators.
autobox::List::Util(3pm)	Bring the List::Util functions to autobox.
autodia(1p)	A perl script using the Autodia modules to create UML Class Diagrams or documents. from code or.
Autodia(3pm)	The configuration and Utility perl module for AutoDia.
autodia(3pm)	A perl script using the Autodia modules to create UML Class Diagrams or documents. from code or.
Autodia::Diagram(3pm)	Class to hold a collection of objects representing parts of a Dia Diagram.
Autodia::Diagram::Class(3pm)	Class that holds, updates and outputs the values of a diagram element of type class.
Autodia::Diagram::Component(3pm)	…
Autodia::Handler(3pm)	Generic language handler superclass.
Autodia::Handler::ASP(3pm)	AutoDia handler for ASP.
Autodia::Handler::Cpp(3pm)	AutoDia handler for C++.
Autodia::Handler::CSharp(3pm)	AutoDia handler for C#.
Autodia::Handler::DBI(3pm)	AutoDia handler for DBI connections.
Autodia::Handler::DBI_SQLT(3pm)	AutoDia handler for DBI connections.
Autodia::Handler::dia(3pm)	AutoDia handler for dia.
Autodia::Handler::Mason(3pm)	Allows Autodia to parse HTML::Mason files.
Autodia::Handler::Perl(3pm)	AutoDia handler for perl.
Autodia::Handler::PHP(3pm)	AutoDia handler for PHP.
Autodia::Handler::SQL(3pm)	AutoDia handler for SQL.
Autodia::Handler::Torque(3pm)	AutoDia handler for Torque xml database schema.
Autodia::Handler::umbrello(3pm)	AutoDia handler for umbrello.
autodie(3pm)	Replace functions with ones that succeed or die with lexical scope.
autodie::exception(3pm)	Exceptions from autodying functions.
autodie::exception::system(3pm)	Exceptions from autodying system().
autodie::hints(3pm)	Provide hints about user subroutines to autodie.
autodie::Scope::Guard(3pm)	Wrapper class for calling subs at end of scope.
autodie::Scope::GuardStack(3pm)	Hook stack for managing scopes via %^H.
autodie::skip(3pm)	Skip a package when throwing autodie exceptions.
autodie::Util(3pm)	Internal Utility subroutines for autodie and Fatal.
AutoSearch(1p)	…
autovivification(3pm)	Lexically disable autovivification.
average_genome_size(1p)	Calculate the average genome size (in bp) of species in a Grinder library.
B::Clobbers(3pm)	Clobbering analyzer.
B::Compiling(3pm)	Expose PL_compiling to perl.
B::ConstOptree(3pm)	Optree constant folding for $^O, $^V, and $].
B::Hooks::EndOfScope(3pm)	Execute code after a scope finished compilation.
B::Hooks::EndOfScope::PP(3pm)	Execute code after a scope finished compilation - PP implementation.
B::Hooks::EndOfScope::XS(3pm)	Execute code after a scope finished compilation - XS implementation.
B::Hooks::OP::Annotation(3pm)	Annotate and delegate hooked OPs.
B::Hooks::OP::Check(3pm)	Wrap OP check callbacks.
B::Hooks::OP::Check::EntersubForCV(3pm)	Invoke callbacks on construction of entersub OPs for certain CVs.
B::Hooks::OP::PPAddr(3pm)	Hook into opcode execution.
B::Hooks::Parser(3pm)	Interface to perl's parser variables.
B::Keywords(3pm)	Lists of reserved barewords and symbol names.
B::Lint(3pm)	Perl lint.
B::Lint::Debug(3pm)	Adds debugging stringification to B::.
B::Module::Info(3pm)	Information about Perl modules.
B::PerlReq(3pm)	Perl compiler backend to extract Perl dependencies.
B::Utils(3pm)	Helper functions for op tree manipulation.
B::Utils::OP(3pm)	Op related utility functions for perl.
B::Walker(3pm)	Dumb walker, optree ranger.
Barcode::Code128(3pm)	Generate CODE 128 bar codes.
Barcode::ZBar(3pm)	Perl interface to the ZBar Barcode Reader.
Barcode::ZBar::Image(3pm)	Image object to scan for bar codes.
Barcode::ZBar::ImageScanner(3pm)	Scan images for bar codes.
Barcode::ZBar::Processor(3pm)	Self-contained bar code reader.
Barcode::ZBar::Symbol(3pm)	Bar code scan result object.
bareword::filehandles(3pm)	Disables bareword filehandles.
basepods(1p)	Print out pod paths for the standard perl manpages.
basic_db_auth(8)	Database auth helper for Squid.
beancounter(1p)	Stock portfolio performance monitor tool.
bed2gff3(1p)	Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into.
Benchmark::Apps(3pm)	Simple interface to benchmark applications.
Benchmark::ProgressBar(3pm)	Display Progress Bar While You Wait For Your Benchmark.
Benchmark::Timer(3pm)	Benchmarking with statistical confidence.
Bencode(3pm)	BitTorrent serialisation format.
BerkeleyDB(3pm)	Perl extension for Berkeley DB version 2, 3, 4 or 5.
Best(3pm)	Load modules with fallback.
bgoffice-dict-download(1)	Download dictionaries for bgoffice.
biber(1p)	A bibtex replacement for users of biblatex.
Biber(3pm)	Main module for biber, a bibtex replacement for users of biblatex.
Biber::Config(3pm)	Configuration items which need to be saved across the.
Biber::Constants(3pm)	Global constants for biber.
Biber::DataModel(3pm)	Biber::DataModel objects.
Biber::Entries(3pm)	Biber::Entries objects.
Biber::Entry(3pm)	Biber::Entry objects.
Biber::Entry::Name(3pm)	Biber::Entry::Name objects.
Biber::Entry::Names(3pm)	Biber::Entry::Names objects.
Biber::Input::file::biblatexml(3pm)	Look in a BibLaTeXML file for an entry and create it if found.
Biber::Input::file::bibtex(3pm)	Look in a BibTeX file for an entry and create it if found.
Biber::Input::file::ris(3pm)	Look in a RIS file for an entry and create it if found.
Biber::Internals(3pm)	Internal methods for processing the bibliographic data.
Biber::LaTeX::Recode(3pm)	Encode/Decode chars to/from UTF-8/lacros in LaTeX.
Biber::Output::base(3pm)	Base class for Biber output modules.
Biber::Output::bbl(3pm)	Class for Biber output of .bbl.
Biber::Output::biblatexml(3pm)	Class for biblatexml output of tool mode.
Biber::Output::bibtex(3pm)	Class for bibtex output.
Biber::Output::dot(3pm)	Class for Biber output of GraphViz .dot files.
Biber::Output::test(3pm)	Output class for loopback testing Essentially, this outputs to a string so we can look.
Biber::Section(3pm)	Biber::Section objects.
Biber::Sections(3pm)	Biber::Sections objects.
Biber::SortList(3pm)	Biber::SortList objects.
Biber::SortLists(3pm)	Biber::SortLists objects.
Biber::UCollate(3pm)	…
Biber::Utils(3pm)	Various utility subs used in Biber.
Biblio::Citation::Parser(3pm)	Citation parsing framework.
Biblio::Citation::Parser::Citebase(3pm)	Citebase's citation parsing module.
Biblio::Citation::Parser::Jiao(3pm)	Citation parsing using Zhuoan Jiao's parsing module.
Biblio::Citation::Parser::Jiao::Utility(3pm)	Perl module containing text processing subroutines.
Biblio::Citation::Parser::Standard(3pm)	Citation parsing functionality.
Biblio::Citation::Parser::Templates(3pm)	Citation templates collection.
Biblio::Citation::Parser::Utils(3pm)	OpenURL utility functions.
Biblio::EndnoteStyle(3pm)	Reference formatting using Endnote-like templates.
Biblio::Isis(3pm)	Read CDS/ISIS, WinISIS and IsisMarc database.
Biblio::Isis::Manual(3pm)	…
Biblio::Thesaurus(3pm)	Perl extension for managing ISO thesaurus.
BIND::Conf_Parser(3pm)	Parser class for BIND configuration files.
BIND::Config::Parser(3pm)	Parse BIND Config file.
Bio::Align::AlignI(3pm)	An interface for describing sequence alignments.
Bio::Align::DNAStatistics(3pm)	Calculate some statistics for a DNA alignment.
Bio::Align::Graphics(3pm)	Graphic Rendering of Bio::Align::AlignI Objects.
Bio::Align::PairwiseStatistics(3pm)	Base statistic object for Pairwise Alignments.
Bio::Align::ProteinStatistics(3pm)	Calculate Protein Alignment statistics (mostly distances).
Bio::Align::StatisticsI(3pm)	Calculate some statistics for an alignment.
Bio::Align::Utilities(3pm)	A collection of utilities regarding converting and manipulating alignment objects.
Bio::AlignIO(3pm)	Handler for AlignIO Formats.
Bio::AlignIO::arp(3pm)	ARP MSA Sequence input/output stream.
Bio::AlignIO::bl2seq(3pm)	Bl2seq sequence input/output stream.
Bio::AlignIO::clustalw(3pm)	Clustalw sequence input/output stream.
Bio::AlignIO::emboss(3pm)	Parse EMBOSS alignment output (from applications water and needle).
Bio::AlignIO::fasta(3pm)	Fasta MSA Sequence input/output stream.
Bio::AlignIO::Handler::GenericAlignHandler(3pm)	Bio::HandlerI-based generic data handler class for.
Bio::AlignIO::largemultifasta(3pm)	Largemultifasta MSA Sequence input/output stream.
Bio::AlignIO::maf(3pm)	Multiple Alignment Format sequence input stream.
Bio::AlignIO::mase(3pm)	Mase sequence input/output stream.
Bio::AlignIO::mega(3pm)	Parse and Create MEGA format data files.
Bio::AlignIO::meme(3pm)	Meme sequence input/output stream.
Bio::AlignIO::metafasta(3pm)	Metafasta MSA Sequence input/output stream.
Bio::AlignIO::msf(3pm)	Msf sequence input/output stream.
Bio::AlignIO::nexml(3pm)	NeXML format sequence alignment input/output stream driver.
Bio::AlignIO::nexus(3pm)	NEXUS format sequence input/output stream.
Bio::AlignIO::pfam(3pm)	Pfam sequence input/output stream.
Bio::AlignIO::phylip(3pm)	PHYLIP format sequence input/output stream.
Bio::AlignIO::po(3pm)	Po MSA Sequence input/output stream.
Bio::AlignIO::proda(3pm)	Proda sequence input/output stream.
Bio::AlignIO::prodom(3pm)	Prodom sequence input/output stream.
Bio::AlignIO::psi(3pm)	Read/Write PSI-BLAST profile alignment files.
Bio::AlignIO::selex(3pm)	Selex sequence input/output stream.
Bio::AlignIO::stockholm(3pm)	Stockholm sequence input/output stream.
Bio::AlignIO::xmfa(3pm)	XMFA MSA Sequence input/output stream.
Bio::AnalysisI(3pm)	An interface to any (local or remote) analysis tool.
Bio::AnalysisParserI(3pm)	Generic analysis output parser interface.
Bio::AnalysisResultI(3pm)	Interface for analysis result objects.
Bio::AnnotatableI(3pm)	The base interface an annotatable object must implement.
Bio::Annotation::AnnotationFactory(3pm)	Instantiates a new Bio::AnnotationI (or derived class) through a factory.
Bio::Annotation::Collection(3pm)	Default Perl implementation of AnnotationCollectionI.
Bio::Annotation::Comment(3pm)	A comment object, holding text.
Bio::Annotation::DBLink(3pm)	Untyped links between databases.
Bio::Annotation::OntologyTerm(3pm)	An ontology term adapted to AnnotationI.
Bio::Annotation::Reference(3pm)	Specialised DBLink object for Literature References.
Bio::Annotation::Relation(3pm)	Relationship (pairwise) with other objects SeqI and NodeI;.
Bio::Annotation::SimpleValue(3pm)	A simple scalar.
Bio::Annotation::StructuredValue(3pm)	A scalar with embedded structured information.
Bio::Annotation::TagTree(3pm)	AnnotationI with tree-like hierarchal key-value relationships ('structured tags').
Bio::Annotation::Target(3pm)	Provides an object which represents a target (ie, a similarity hit) from one object.
Bio::Annotation::Tree(3pm)	Provide a tree as an annotation to a Bio::AnnotatableI object.
Bio::Annotation::TypeManager(3pm)	Manages types for annotation collections.
Bio::AnnotationCollectionI(3pm)	Interface for annotation collections.
Bio::AnnotationI(3pm)	Annotation interface.
Bio::ASN1::EntrezGene(3pm)	Regular expression-based Perl Parser for NCBI Entrez Gene.
Bio::ASN1::EntrezGene::Indexer(3pm)	Indexes NCBI Sequence files.
Bio::ASN1::Sequence(3pm)	Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
Bio::ASN1::Sequence::Indexer(3pm)	Indexes NCBI Sequence files.
Bio::Assembly::Contig(3pm)	Perl module to hold and manipulate.
Bio::Assembly::ContigAnalysis(3pm)	…
Bio::Assembly::IO(3pm)	Handler for Assembly::IO Formats.
Bio::Assembly::IO::ace(3pm)	Module to load ACE files from various assembly programs.
Bio::Assembly::IO::bowtie(3pm)	An IO module for assemblies in Bowtie format BETA.
Bio::Assembly::IO::maq(3pm)	Driver to read assembly files in maq format BETA.
Bio::Assembly::IO::phrap(3pm)	Driver to load phrap.out files.
Bio::Assembly::IO::sam(3pm)	An IO module for assemblies in Sam format BETA.
Bio::Assembly::IO::tigr(3pm)	Driver to read and write assembly files in the TIGR Assembler v2 default format.
Bio::Assembly::Scaffold(3pm)	Perl module to hold and manipulate sequence assembly data.
Bio::Assembly::ScaffoldI(3pm)	Abstract Inteface of Sequence Assemblies.
Bio::Assembly::Singlet(3pm)	Perl module to hold and manipulate.
Bio::Assembly::Tools::ContigSpectrum(3pm)	Create and manipulate contig spectra.
Bio::Chado::NaturalDiversity::Reports(3pm)	Collection of functions for formatting Chado stock related data.
Bio::Chado::Schema(3pm)	A standard DBIx::Class layer for the Chado database schema.
Bio::Chado::Schema::Test(3pm)	Library to be used by Bio::Chado::Schema test scripts.
Bio::Chado::Schema::Util(3pm)	Utility functions shared by Bio::Chado::Schema objects.
Bio::Cluster::ClusterFactory(3pm)	Instantiates a new Bio::ClusterI (or derived class) through a factory.
Bio::Cluster::FamilyI(3pm)	Family Interface.
Bio::Cluster::SequenceFamily(3pm)	Sequence Family object.
Bio::Cluster::UniGene(3pm)	UniGene object.
Bio::Cluster::UniGeneI(3pm)	Abstract interface of UniGene object.
Bio::ClusterI(3pm)	Cluster Interface.
Bio::ClusterIO(3pm)	Handler for Cluster Formats.
Bio::ClusterIO::dbsnp(3pm)	DbSNP input stream.
Bio::ClusterIO::unigene(3pm)	UniGene input stream.
Bio::CodonUsage::IO(3pm)	For reading and writing codon usage tables to file.
Bio::CodonUsage::Table(3pm)	For access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::Coordinate::Chain(3pm)	…
Bio::Coordinate::Collection(3pm)	…
Bio::Coordinate::ExtrapolatingPair(3pm)	…
Bio::Coordinate::GeneMapper(3pm)	…
Bio::Coordinate::Graph(3pm)	…
Bio::Coordinate::MapperI(3pm)	…
Bio::Coordinate::Pair(3pm)	…
Bio::Coordinate::Result(3pm)	…
Bio::Coordinate::Result::Gap(3pm)	…
Bio::Coordinate::Result::Match(3pm)	…
Bio::Coordinate::ResultI(3pm)	…
Bio::Coordinate::Utils(3pm)	…
Bio::Das::FeatureTypeI(3pm)	Simple interface to Sequence Ontology feature types.
Bio::Das::Lite(3pm)	Perl extension for the DAS (HTTP+XML) Protocol (http://biodas.org/).
Bio::Das::SegmentI(3pm)	DAS-style access to a feature database.
Bio::DasI(3pm)	DAS-style access to a feature database.
Bio::DB::Ace(3pm)	Database object interface to ACeDB servers.
Bio::DB::Bam::Alignment(3pm)	…
Bio::DB::Bam::AlignWrapper(3pm)	…
Bio::DB::Bam::Pileup(3pm)	…
Bio::DB::Bam::PileupWrapper(3pm)	…
Bio::DB::Bam::Query(3pm)	…
Bio::DB::Bam::Target(3pm)	…
Bio::DB::BioFetch(3pm)	Database object interface to BioFetch retrieval.
Bio::DB::CUTG(3pm)	For access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::DB::DBFetch(3pm)	Database object for retrieving using the dbfetch script.
Bio::DB::EMBL(3pm)	Database object interface for EMBL entry retrieval.
Bio::DB::EntrezGene(3pm)	Database object interface to Entrez Gene.
Bio::DB::ESoap(3pm)	Client for the NCBI Entrez EUtilities SOAP server.
Bio::DB::ESoap::WSDL(3pm)	WSDL parsing for Entrez SOAP EUtilities.
Bio::DB::Expression(3pm)	DESCRIPTION of Object.
Bio::DB::Expression::geo(3pm)	*** DESCRIPTION of Class.
Bio::DB::Failover(3pm)	A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs.
Bio::DB::Fasta(3pm)	Fast indexed access to fasta files.
Bio::DB::FileCache(3pm)	In file cache for BioSeq objects.
Bio::DB::Flat(3pm)	Interface for indexed flat files.
Bio::DB::Flat::BDB(3pm)	Interface for BioHackathon standard BDB-indexed flat file.
Bio::DB::Flat::BDB::embl(3pm)	Embl adaptor for Open-bio standard BDB-indexed flat file.
Bio::DB::Flat::BDB::fasta(3pm)	Fasta adaptor for Open-bio standard BDB-indexed flat file.
Bio::DB::Flat::BDB::genbank(3pm)	Genbank adaptor for Open-bio standard BDB-indexed flat file.
Bio::DB::Flat::BDB::swiss(3pm)	Swissprot adaptor for Open-bio standard BDB-indexed flat file.
Bio::DB::Flat::BinarySearch(3pm)	BinarySearch search indexing system for sequence files.
Bio::DB::GenBank(3pm)	Database object interface to GenBank.
Bio::DB::GenericWebAgent(3pm)	Helper base class for parameter-based remote server access and response retrieval.
Bio::DB::GenPept(3pm)	Database object interface to GenPept.
Bio::DB::GFF(3pm)	…
Bio::DB::GFF::Adaptor::ace(3pm)	…
Bio::DB::GFF::Adaptor::berkeleydb(3pm)	…
Bio::DB::GFF::Adaptor::berkeleydb::iterator(3pm)	Iterator for Bio::DB::GFF::Adaptor::berkeleydb.
Bio::DB::GFF::Adaptor::biofetch(3pm)	…
Bio::DB::GFF::Adaptor::biofetch_oracle(3pm)	…
Bio::DB::GFF::Adaptor::dbi(3pm)	…
Bio::DB::GFF::Adaptor::dbi::caching_handle(3pm)	…
Bio::DB::GFF::Adaptor::dbi::iterator(3pm)	Iterator for Bio::DB::GFF::Adaptor::dbi.
Bio::DB::GFF::Adaptor::dbi::mysql(3pm)	…
Bio::DB::GFF::Adaptor::dbi::mysqlace(3pm)	…
Bio::DB::GFF::Adaptor::dbi::mysqlcmap(3pm)	…
Bio::DB::GFF::Adaptor::dbi::mysqlopt(3pm)	…
Bio::DB::GFF::Adaptor::dbi::oracle(3pm)	…
Bio::DB::GFF::Adaptor::dbi::oracleace(3pm)	…
Bio::DB::GFF::Adaptor::dbi::pg(3pm)	…
Bio::DB::GFF::Adaptor::dbi::pg_fts(3pm)	…
Bio::DB::GFF::Adaptor::memory(3pm)	…
Bio::DB::GFF::Adaptor::memory::feature_serializer(3pm)	Utility methods for serializing and deserializing GFF.
Bio::DB::GFF::Adaptor::memory::iterator(3pm)	Iterator for Bio::DB::GFF::Adaptor::memory.
Bio::DB::GFF::Aggregator(3pm)	…
Bio::DB::GFF::Aggregator::alignment(3pm)	…
Bio::DB::GFF::Aggregator::clone(3pm)	…
Bio::DB::GFF::Aggregator::coding(3pm)	…
Bio::DB::GFF::Aggregator::gene(3pm)	…
Bio::DB::GFF::Aggregator::match(3pm)	…
Bio::DB::GFF::Aggregator::match_gap(3pm)	…
Bio::DB::GFF::Aggregator::none(3pm)	…
Bio::DB::GFF::Aggregator::orf(3pm)	…
Bio::DB::GFF::Aggregator::processed_transcript(3pm)	…
Bio::DB::GFF::Aggregator::reftranscript(3pm)	…
Bio::DB::GFF::Aggregator::so_transcript(3pm)	…
Bio::DB::GFF::Aggregator::transcript(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_acembly(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_ensgene(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_genscan(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_refgene(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_sanger22(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_softberry(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_twinscan(3pm)	…
Bio::DB::GFF::Aggregator::ucsc_unigene(3pm)	…
Bio::DB::GFF::Aggregator::waba_alignment(3pm)	…
Bio::DB::GFF::Aggregator::wormbase_gene(3pm)	…
Bio::DB::GFF::Featname(3pm)	…
Bio::DB::GFF::Feature(3pm)	…
Bio::DB::GFF::Homol(3pm)	…
Bio::DB::GFF::RelSegment(3pm)	…
Bio::DB::GFF::Segment(3pm)	…
Bio::DB::GFF::Typename(3pm)	…
Bio::DB::GFF::Util::Binning(3pm)	Binning utility for Bio::DB::GFF index.
Bio::DB::GFF::Util::Rearrange(3pm)	Rearrange utility.
Bio::DB::HIV(3pm)	Database object interface to the Los Alamos HIV Sequence Database.
Bio::DB::HIV::HIVAnnotProcessor(3pm)	Adds HIV-specific annotations to Bio::SeqIO streams.
Bio::DB::HIV::HIVQueryHelper(3pm)	Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery.
Bio::DB::IndexedBase(3pm)	Base class for modules using indexed sequence files.
Bio::DB::InMemoryCache(3pm)	Abstract interface for a sequence database.
Bio::DB::LocationI(3pm)	A RandomAccessI-like abstract interface for retrieving location data from a sequence.
Bio::DB::MeSH(3pm)	Term retrieval from a Web MeSH database.
Bio::DB::NCBIHelper(3pm)	A collection of routines useful for queries to NCBI databases.
Bio::DB::Qual(3pm)	Fast indexed access to quality files.
Bio::DB::Query::GenBank(3pm)	Build a GenBank Entrez Query.
Bio::DB::Query::HIVQuery(3pm)	Query interface to the Los Alamos HIV Sequence Database.
Bio::DB::Query::WebQuery(3pm)	Helper class for web-based sequence queryies.
Bio::DB::QueryI(3pm)	Object Interface to queryable sequence databases.
Bio::DB::RandomAccessI(3pm)	Abstract interface for a sequence database.
Bio::DB::ReferenceI(3pm)	A RandomAccessI-like abstract interface for retrieving Reference data from a sequence.
Bio::DB::RefSeq(3pm)	Database object interface for RefSeq retrieval.
Bio::DB::Registry(3pm)	Access to the Open Bio Database Access registry scheme.
Bio::DB::Sam(3pm)	…
Bio::DB::Sam::Constants(3pm)	…
Bio::DB::SeqFeature(3pm)	…
Bio::DB::SeqFeature::NormalizedFeature(3pm)	…
Bio::DB::SeqFeature::NormalizedFeatureI(3pm)	…
Bio::DB::SeqFeature::NormalizedTableFeatureI(3pm)	…
Bio::DB::SeqFeature::Segment(3pm)	…
Bio::DB::SeqFeature::Store(3pm)	…
Bio::DB::SeqFeature::Store::Alias(3pm)	…
Bio::DB::SeqFeature::Store::bdb(3pm)	Fetch and store objects from a BerkeleyDB.
Bio::DB::SeqFeature::Store::berkeleydb(3pm)	…
Bio::DB::SeqFeature::Store::berkeleydb3(3pm)	…
Bio::DB::SeqFeature::Store::DBI::Iterator(3pm)	Utility methods for creating and iterating over SeqFeature records.
Bio::DB::SeqFeature::Store::DBI::mysql(3pm)	…
Bio::DB::SeqFeature::Store::DBI::Pg(3pm)	…
Bio::DB::SeqFeature::Store::DBI::SQLite(3pm)	…
Bio::DB::SeqFeature::Store::FeatureFileLoader(3pm)	…
Bio::DB::SeqFeature::Store::GFF2Loader(3pm)	…
Bio::DB::SeqFeature::Store::GFF3Loader(3pm)	…
Bio::DB::SeqFeature::Store::Loader(3pm)	…
Bio::DB::SeqFeature::Store::LoadHelper(3pm)	…
Bio::DB::SeqFeature::Store::memory(3pm)	…
Bio::DB::SeqHound(3pm)	Database object interface to SeqHound.
Bio::DB::SeqI(3pm)	Abstract Interface for Sequence databases.
Bio::DB::SeqVersion(3pm)	Front end to querying databases for identifier versions.
Bio::DB::SeqVersion::gi(3pm)	Interface to NCBI Sequence Revision History page.
Bio::DB::SoapEUtilities(3pm)	Interface to the NCBI Entrez web service BETA.
Bio::DB::SoapEUtilities::DocSumAdaptor(3pm)	Handle for Entrez SOAP DocSums.
Bio::DB::SoapEUtilities::FetchAdaptor(3pm)	Conversion of Entrez SOAP messages to BioPerl objects.
Bio::DB::SoapEUtilities::FetchAdaptor::seq(3pm)	Fetch adaptor for 'seq' efetch SOAP messages.
Bio::DB::SoapEUtilities::FetchAdaptor::species(3pm)	Fetch adaptor for 'taxonomy' efetch SOAP messages.
Bio::DB::SoapEUtilities::GQueryAdaptor(3pm)	Handle for Entrez SOAP GlobalQuery items.
Bio::DB::SoapEUtilities::LinkAdaptor(3pm)	Handle for Entrez SOAP LinkSets.
Bio::DB::SoapEUtilities::Result(3pm)	Accessor object for SoapEUtilities results.
Bio::DB::SwissProt(3pm)	Database object interface to SwissProt retrieval.
Bio::DB::Tagger(3pm)	…
Bio::DB::Tagger::Tag(3pm)	…
Bio::DB::Taxonomy(3pm)	Access to a taxonomy database.
Bio::DB::Taxonomy::entrez(3pm)	Taxonomy Entrez driver.
Bio::DB::Taxonomy::flatfile(3pm)	Use the NCBI taxonomy from local indexed flat files.
Bio::DB::Taxonomy::greengenes(3pm)	Use the Greengenes taxonomy.
Bio::DB::Taxonomy::list(3pm)	An implementation of Bio::DB::Taxonomy that accepts lists of words to build a.
Bio::DB::Taxonomy::silva(3pm)	Use the Silva taxonomy.
Bio::DB::TFBS(3pm)	Access to a Transcription Factor Binding Site database.
Bio::DB::TFBS::transfac_pro(3pm)	An implementation of Bio::DB::TFBS which uses local flat files for transfac pro.
Bio::DB::Universal(3pm)	Artificial database that delegates to specific databases.
Bio::DB::UpdateableSeqI(3pm)	An interface for writing to a database of sequences.
Bio::DB::WebDBSeqI(3pm)	Object Interface to generalize Web Databases for retrieving sequences.
Bio::DBLinkContainerI(3pm)	Abstract interface for any object wanting to use.
Bio::DescribableI(3pm)	Interface for objects with human readable names and descriptions.
Bio::Draw::Pictogram(3pm)	Generate SVG output of Pictogram display for consensus motifs.
Bio::Event::EventGeneratorI(3pm)	This interface describes the basic event generator class.
Bio::Event::EventHandlerI(3pm)	An Event Handler Interface.
Bio::Factory::AnalysisI(3pm)	An interface to analysis tool factory.
Bio::Factory::ApplicationFactoryI(3pm)	Interface class for Application Factories.
Bio::Factory::DriverFactory(3pm)	Base class for factory classes loading drivers.
Bio::Factory::EMBOSS(3pm)	EMBOSS application factory class.
Bio::Factory::FTLocationFactory(3pm)	A FeatureTable Location Parser.
Bio::Factory::LocationFactoryI(3pm)	A factory interface for generating locations from a string.
Bio::Factory::MapFactoryI(3pm)	A Factory for getting markers.
Bio::Factory::ObjectBuilderI(3pm)	Interface for an object builder.
Bio::Factory::ObjectFactory(3pm)	Instantiates a new Bio::Root::RootI (or derived class) through a factory.
Bio::Factory::ObjectFactoryI(3pm)	A General object creator factory.
Bio::Factory::SeqAnalysisParserFactory(3pm)	Class capable of creating SeqAnalysisParserI compliant parsers.
Bio::Factory::SeqAnalysisParserFactoryI(3pm)	Interface describing objects capable.
Bio::Factory::SequenceFactoryI(3pm)	This interface allows for generic building of sequences in factories which.
Bio::Factory::SequenceProcessorI(3pm)	Interface for chained sequence.
Bio::Factory::SequenceStreamI(3pm)	Interface describing the basics of a Sequence Stream.
Bio::Factory::TreeFactoryI(3pm)	Factory Interface for getting and writing trees.
Bio::FeatureHolderI(3pm)	The base interface an object with features must implement.
Bio::Graphics(3pm)	Generate GD images of Bio::Seq objects.
Bio::Graphics::Browser2::AuthorizedFeatureFile(3pm)	…
Bio::Graphics::Browser2::CAlign(3pm)	Compiled helper for Bio::Graphics::Browser::Realign.
Bio::Graphics::Browser2::DataBase(3pm)	…
Bio::Graphics::Browser2::DataSource(3pm)	…
Bio::Graphics::Browser2::GFFhelper(3pm)	…
Bio::Graphics::Browser2::Markup(3pm)	Markup routines for sequences in text form.
Bio::Graphics::Browser2::OptionPick(3pm)	…
Bio::Graphics::Browser2::PadAlignment(3pm)	Insert pads into a multiple alignment.
Bio::Graphics::Browser2::Plugin(3pm)	…
Bio::Graphics::Browser2::Plugin::AuthPlugin(3pm)	…
Bio::Graphics::Browser2::PluginSet(3pm)	…
Bio::Graphics::Browser2::Realign(3pm)	Perl extension for Smith-Waterman alignments.
Bio::Graphics::Browser2::Region(3pm)	…
Bio::Graphics::Browser2::RegionSearch(3pm)	…
Bio::Graphics::Browser2::RemoteSet(3pm)	…
Bio::Graphics::Browser2::Render(3pm)	…
Bio::Graphics::Browser2::RenderPanels(3pm)	…
Bio::Graphics::Browser2::Util(3pm)	…
Bio::Graphics::ConfiguratorI(3pm)	A sectioned map of configuration options (a map of maps), with a default.
Bio::Graphics::DrawTransmembrane(3pm)	Draw a cartoon of an Alpha-helical transmembrane protein.
Bio::Graphics::Feature(3pm)	A simple feature object for use with Bio::Graphics::Panel.
Bio::Graphics::FeatureBase(3pm)	Compatibility module.
Bio::Graphics::FeatureDir(3pm)	…
Bio::Graphics::FeatureFile(3pm)	…
Bio::Graphics::FeatureFile::Iterator(3pm)	…
Bio::Graphics::Glyph(3pm)	Base class for Bio::Graphics::Glyph objects.
Bio::Graphics::Glyph::alignment(3pm)	The "alignment" glyph.
Bio::Graphics::Glyph::allele_tower(3pm)	The "allele_tower" glyph.
Bio::Graphics::Glyph::anchored_arrow(3pm)	The "anchored_arrow" glyph.
Bio::Graphics::Glyph::arrow(3pm)	The "arrow" glyph.
Bio::Graphics::Glyph::box(3pm)	The "box" glyph.
Bio::Graphics::Glyph::broken_line(3pm)	The "broken line" glyph.
Bio::Graphics::Glyph::cds(3pm)	The "cds" glyph.
Bio::Graphics::Glyph::christmas_arrow(3pm)	The "christmas arrow" glyph.
Bio::Graphics::Glyph::crossbox(3pm)	The "crossbox" glyph.
Bio::Graphics::Glyph::dashed_line(3pm)	The "dashed line" glyph.
Bio::Graphics::Glyph::decorated_gene(3pm)	A GFF3-compatible gene glyph with protein decorations.
Bio::Graphics::Glyph::decorated_transcript(3pm)	Draws processed transcript with protein decorations.
Bio::Graphics::Glyph::diamond(3pm)	The "diamond" glyph.
Bio::Graphics::Glyph::dna(3pm)	The "dna" glyph.
Bio::Graphics::Glyph::dot(3pm)	The "dot" glyph.
Bio::Graphics::Glyph::dumbbell(3pm)	A glyph that draws a "dumbbell" with the same shapes on both ends.
Bio::Graphics::Glyph::ellipse(3pm)	The "ellipse" glyph.
Bio::Graphics::Glyph::ex(3pm)	The "ex", or "crossed box" glyph.
Bio::Graphics::Glyph::extending_arrow(3pm)	…
Bio::Graphics::Glyph::Factory(3pm)	Factory for Bio::Graphics::Glyph objects.
Bio::Graphics::Glyph::fb_shmiggle(3pm)	…
Bio::Graphics::Glyph::fixedwidth(3pm)	A base class fixed width glyphs.
Bio::Graphics::Glyph::flag(3pm)	The "flag" glyph.
Bio::Graphics::Glyph::gene(3pm)	A GFF3-compatible gene glyph.
Bio::Graphics::Glyph::generic(3pm)	The "generic" glyph.
Bio::Graphics::Glyph::graded_segments(3pm)	The "graded_segments" glyph.
Bio::Graphics::Glyph::group(3pm)	The "group" glyph.
Bio::Graphics::Glyph::hat(3pm)	The "hat" glyph.
Bio::Graphics::Glyph::heat_map(3pm)	The "heat_map" glyph.
Bio::Graphics::Glyph::heat_map_ideogram(3pm)	The "heat_map_ideogram" glyph.
Bio::Graphics::Glyph::heterogeneous_segments(3pm)	The "heterogeneous_segments" glyph.
Bio::Graphics::Glyph::hidden(3pm)	The "hidden" glyph.
Bio::Graphics::Glyph::hybrid_plot(3pm)	An xyplot plot drawing dual graph using data from two or more wiggle files.
Bio::Graphics::Glyph::ideogram(3pm)	The "ideogram" glyph.
Bio::Graphics::Glyph::image(3pm)	A glyph that draws photographs & other images.
Bio::Graphics::Glyph::lightning(3pm)	The "lightning" glyph.
Bio::Graphics::Glyph::line(3pm)	The "line" glyph.
Bio::Graphics::Glyph::merge_parts(3pm)	A base class which suppors semantic zooming of scored alignment features.
Bio::Graphics::Glyph::merged_alignment(3pm)	The "merged_alignment" glyph.
Bio::Graphics::Glyph::minmax(3pm)	The minmax glyph.
Bio::Graphics::Glyph::operon(3pm)	The "polycistronic operon" glyph.
Bio::Graphics::Glyph::oval(3pm)	The "oval" glyph.
Bio::Graphics::Glyph::pairplot(3pm)	The "pairwise plot" glyph.
Bio::Graphics::Glyph::pentagram(3pm)	The "pentagram" glyph.
Bio::Graphics::Glyph::phylo_align(3pm)	The "phylogenetic alignment" glyph.
Bio::Graphics::Glyph::pinsertion(3pm)	The "Drosophila P-element Insertion" glyph.
Bio::Graphics::Glyph::primers(3pm)	The "STS primers" glyph.
Bio::Graphics::Glyph::processed_transcript(3pm)	The sequence ontology transcript glyph.
Bio::Graphics::Glyph::protein(3pm)	The "protein" glyph.
Bio::Graphics::Glyph::ragged_ends(3pm)	The "ragged ends" glyph.
Bio::Graphics::Glyph::rainbow_gene(3pm)	A GFF3-compatible gene glyph.
Bio::Graphics::Glyph::redgreen_box(3pm)	The "redgreen_box" glyph.
Bio::Graphics::Glyph::redgreen_segment(3pm)	The "redgreen_segments" glyph.
Bio::Graphics::Glyph::repeating_shape(3pm)	A glyph that draws the same shape repeatedly.
Bio::Graphics::Glyph::rndrect(3pm)	The "round rect" glyph.
Bio::Graphics::Glyph::ruler_arrow(3pm)	Glyph for drawing an arrow as ruler (5' and 3' are marked as label).
Bio::Graphics::Glyph::saw_teeth(3pm)	The "saw teeth" glyph.
Bio::Graphics::Glyph::scale(3pm)	The "scale" glyph.
Bio::Graphics::Glyph::segmented_keyglyph(3pm)	The "segmented_keyglyph" glyph.
Bio::Graphics::Glyph::segments(3pm)	The "segments" glyph.
Bio::Graphics::Glyph::so_transcript(3pm)	The sequence ontology transcript glyph.
Bio::Graphics::Glyph::span(3pm)	The "span" glyph.
Bio::Graphics::Glyph::spectrogram(3pm)	The "spectrogram" glyph.
Bio::Graphics::Glyph::splice_site(3pm)	The "splice_site" glyph.
Bio::Graphics::Glyph::stackedplot(3pm)	The stackedplot glyph.
Bio::Graphics::Glyph::ternary_plot(3pm)	Draw ternary plot data.
Bio::Graphics::Glyph::text_in_box(3pm)	The "text in box" glyph.
Bio::Graphics::Glyph::three_letters(3pm)	DAS-compatible package to use for drawing a line of groups of three.
Bio::Graphics::Glyph::tic_tac_toe(3pm)	The "tic-tac-toe" glyph.
Bio::Graphics::Glyph::toomany(3pm)	The "too many to show" glyph.
Bio::Graphics::Glyph::trace(3pm)	A glyph that visualizes a trace file.
Bio::Graphics::Glyph::track(3pm)	The "track" glyph.
Bio::Graphics::Glyph::transcript(3pm)	The "transcript" glyph.
Bio::Graphics::Glyph::transcript2(3pm)	The "transcript2" glyph.
Bio::Graphics::Glyph::translation(3pm)	The "6-frame translation" glyph.
Bio::Graphics::Glyph::triangle(3pm)	The "triangle" glyph.
Bio::Graphics::Glyph::two_bolts(3pm)	The "two bolts" glyph.
Bio::Graphics::Glyph::vista_plot(3pm)	The "vista_plot" glyph.
Bio::Graphics::Glyph::wave(3pm)	The "wave" glyph.
Bio::Graphics::Glyph::weighted_arrow(3pm)	The "weighted arrow" glyph.
Bio::Graphics::Glyph::whiskerplot(3pm)	The whiskerplot glyph.
Bio::Graphics::Glyph::wiggle_box(3pm)	A generic box glyph compatible with dense "wig"data.
Bio::Graphics::Glyph::wiggle_density(3pm)	A density plot compatible with dense "wig"data.
Bio::Graphics::Glyph::wiggle_xyplot(3pm)	An xyplot plot compatible with dense "wig"data.
Bio::Graphics::Glyph::xyplot(3pm)	The xyplot glyph.
Bio::Graphics::Panel(3pm)	Generate GD images of Bio::Seq objects.
Bio::Graphics::Pictogram(3pm)	Generate SVG output of Pictogram display for consensus motifs.
Bio::Graphics::RendererI(3pm)	A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI.
Bio::Graphics::Util(3pm)	Non-object-oriented utilities used in Bio::Graphics modules.
Bio::Graphics::Wiggle(3pm)	…
Bio::Graphics::Wiggle::Loader(3pm)	…
Bio::HandlerBaseI(3pm)	Interface class for handler methods which interact with any event-driven parsers.
Bio::IdCollectionI(3pm)	Interface for objects with multiple identifiers.
Bio::IdentifiableI(3pm)	Interface for objects with identifiers.
Bio::Index::Abstract(3pm)	Abstract interface for indexing a flat file.
Bio::Index::AbstractSeq(3pm)	Base class for AbstractSeq.
Bio::Index::Blast(3pm)	Indexes Blast reports and supports retrieval based on query accession(s).
Bio::Index::BlastTable(3pm)	Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on.
Bio::Index::EMBL(3pm)	Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot.
Bio::Index::Fasta(3pm)	Interface for indexing (multiple) fasta files.
Bio::Index::Fastq(3pm)	Interface for indexing (multiple) fastq files.
Bio::Index::GenBank(3pm)	Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
Bio::Index::Hmmer(3pm)	Indexes HMMER reports and supports retreival based on query.
Bio::Index::Qual(3pm)	Interface for indexing (multiple) fasta qual files.
Bio::Index::Stockholm(3pm)	…
Bio::Index::SwissPfam(3pm)	Interface for indexing swisspfam files.
Bio::Index::Swissprot(3pm)	Interface for indexing one or more Swissprot files.
Bio::Installer::Clustalw(3pm)	DESCRIPTION of Object.
Bio::Installer::EMBOSS(3pm)	DESCRIPTION of Object.
Bio::Installer::Generic(3pm)	DESCRIPTION of Object.
Bio::Installer::Hyphy(3pm)	DESCRIPTION of Object.
Bio::Installer::Muscle(3pm)	DESCRIPTION of Object.
Bio::Installer::PAML(3pm)	DESCRIPTION of Object.
Bio::Installer::Probcons(3pm)	DESCRIPTION of Object.
Bio::Installer::SLR(3pm)	DESCRIPTION of Object.
Bio::Installer::TCoffee(3pm)	DESCRIPTION of Object.
Bio::LiveSeq::AARange(3pm)	AARange abstract class for LiveSeq.
Bio::LiveSeq::Chain(3pm)	DoubleChain DataStructure for Perl.
Bio::LiveSeq::ChainI(3pm)	Double linked chain data structure.
Bio::LiveSeq::DNA(3pm)	DNA object for LiveSeq.
Bio::LiveSeq::Exon(3pm)	Range abstract class for LiveSeq.
Bio::LiveSeq::Gene(3pm)	Range abstract class for LiveSeq.
Bio::LiveSeq::Intron(3pm)	Range abstract class for LiveSeq.
Bio::LiveSeq::IO::BioPerl(3pm)	Loader for LiveSeq from EMBL entries with BioPerl.
Bio::LiveSeq::IO::Loader(3pm)	Parent Loader for LiveSeq.
Bio::LiveSeq::Mutation(3pm)	Mutation event descriptor class.
Bio::LiveSeq::Mutator(3pm)	Package mutating LiveSequences.
Bio::LiveSeq::Prim_Transcript(3pm)	Prim_Transcript class for LiveSeq.
Bio::LiveSeq::Range(3pm)	Range abstract class for LiveSeq.
Bio::LiveSeq::Repeat_Region(3pm)	Repeat_Region class for LiveSeq.
Bio::LiveSeq::Repeat_Unit(3pm)	Repeat_Unit class for LiveSeq.
Bio::LiveSeq::SeqI(3pm)	Abstract sequence interface class for LiveSeq.
Bio::LiveSeq::Transcript(3pm)	Transcript class for LiveSeq.
Bio::LiveSeq::Translation(3pm)	Translation class for LiveSeq.
Bio::LocatableSeq(3pm)	A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or.
Bio::Location::Atomic(3pm)	Implementation of a Atomic Location on a Sequence.
Bio::Location::AvWithinCoordPolicy(3pm)	Class implementing Bio::Location::CoordinatePolicy as the average for.
Bio::Location::CoordinatePolicyI(3pm)	Abstract interface for objects implementing a certain policy of computing.
Bio::Location::Fuzzy(3pm)	Implementation of a Location on a Sequence which has unclear start and/or end locations.
Bio::Location::FuzzyLocationI(3pm)	Abstract interface of a Location on a Sequence which has unclear start/end.
Bio::Location::NarrowestCoordPolicy(3pm)	Class implementing Bio::Location::CoordinatePolicy as the narrowest.
Bio::Location::Simple(3pm)	Implementation of a Simple Location on a Sequence.
Bio::Location::Split(3pm)	Implementation of a Location on a Sequence which has multiple locations (start/end.
Bio::Location::SplitLocationI(3pm)	Abstract interface of a Location on a Sequence which has multiple locations.
Bio::Location::WidestCoordPolicy(3pm)	Class implementing Bio::Location::CoordinatePolicy as the widest possible.
Bio::LocationI(3pm)	Abstract interface of a Location on a Sequence.
Bio::MAGE(3pm)	Container module for classes in the MAGE package: MAGE.
Bio::MAGE::Array(3pm)	Container module for classes in the MAGE package: Array.
Bio::MAGE::Array::Array(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ArrayGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ArrayManufacture(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ArrayManufactureDeviation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::FeatureDefect(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::Fiducial(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ManufactureLIMS(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ManufactureLIMSBiomaterial(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::PositionDelta(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Array::ZoneDefect(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign(3pm)	Container module for classes in the MAGE package: ArrayDesign.
Bio::MAGE::ArrayDesign::ArrayDesign(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::CompositeGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::DesignElementGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::FeatureGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::PhysicalArrayDesign(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::ReporterGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::Zone(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::ZoneGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::ArrayDesign::ZoneLayout(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Association(3pm)	…
Bio::MAGE::AuditAndSecurity(3pm)	Container module for classes in the MAGE package: AuditAndSecurity.
Bio::MAGE::AuditAndSecurity::Audit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::AuditAndSecurity::Contact(3pm)	Class for the MAGE-OM API.
Bio::MAGE::AuditAndSecurity::Organization(3pm)	Class for the MAGE-OM API.
Bio::MAGE::AuditAndSecurity::Person(3pm)	Class for the MAGE-OM API.
Bio::MAGE::AuditAndSecurity::Security(3pm)	Class for the MAGE-OM API.
Bio::MAGE::AuditAndSecurity::SecurityGroup(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Base(3pm)	Generic base class.
Bio::MAGE::BioAssay(3pm)	Container module for classes in the MAGE package: BioAssay.
Bio::MAGE::BioAssay::BioAssay(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::BioAssayCreation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::BioAssayTreatment(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::Channel(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::DerivedBioAssay(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::FeatureExtraction(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::Hybridization(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::Image(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::ImageAcquisition(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::MeasuredBioAssay(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssay::PhysicalBioAssay(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData(3pm)	Container module for classes in the MAGE package: BioAssayData.
Bio::MAGE::BioAssayData::BioAssayData(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioAssayDatum(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioAssayDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioAssayMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioAssayMapping(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioDataCube(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioDataTuples(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::BioDataValues(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::CompositeSequenceDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::DerivedBioAssayData(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::DesignElementDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::DesignElementMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::DesignElementMapping(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::FeatureDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::MeasuredBioAssayData(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::QuantitationTypeDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::QuantitationTypeMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::QuantitationTypeMapping(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::ReporterDimension(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioAssayData::Transformation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioEvent(3pm)	Container module for classes in the MAGE package: BioEvent.
Bio::MAGE::BioEvent::BioEvent(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioEvent::Map(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial(3pm)	Container module for classes in the MAGE package: BioMaterial.
Bio::MAGE::BioMaterial::BioMaterial(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::BioMaterialMeasurement(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::BioSample(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::BioSource(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::Compound(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::CompoundMeasurement(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::LabeledExtract(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioMaterial::Treatment(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioSequence(3pm)	Container module for classes in the MAGE package: BioSequence.
Bio::MAGE::BioSequence::BioSequence(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioSequence::SeqFeature(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioSequence::SeqFeatureLocation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BioSequence::SequencePosition(3pm)	Class for the MAGE-OM API.
Bio::MAGE::BQS(3pm)	Container module for classes in the MAGE package: BQS.
Bio::MAGE::BQS::BibliographicReference(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Describable(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Description(3pm)	Container module for classes in the MAGE package: Description.
Bio::MAGE::Description::Database(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Description::DatabaseEntry(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Description::Description(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Description::ExternalReference(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Description::OntologyEntry(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement(3pm)	Container module for classes in the MAGE package: DesignElement.
Bio::MAGE::DesignElement::CompositeCompositeMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::CompositePosition(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::CompositeSequence(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::DesignElement(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::Feature(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::FeatureInformation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::FeatureLocation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::FeatureReporterMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::MismatchInformation(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::Position(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::Reporter(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::ReporterCompositeMap(3pm)	Class for the MAGE-OM API.
Bio::MAGE::DesignElement::ReporterPosition(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Experiment(3pm)	Container module for classes in the MAGE package: Experiment.
Bio::MAGE::Experiment::Experiment(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Experiment::ExperimentalFactor(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Experiment::ExperimentDesign(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Experiment::FactorValue(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Extendable(3pm)	Class for the MAGE-OM API.
Bio::MAGE::HigherLevelAnalysis(3pm)	Container module for classes in the MAGE package: HigherLevelAnalysis.
Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster(3pm)	Class for the MAGE-OM API.
Bio::MAGE::HigherLevelAnalysis::Node(3pm)	Class for the MAGE-OM API.
Bio::MAGE::HigherLevelAnalysis::NodeContents(3pm)	Class for the MAGE-OM API.
Bio::MAGE::HigherLevelAnalysis::NodeValue(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Identifiable(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement(3pm)	Container module for classes in the MAGE package: Measurement.
Bio::MAGE::Measurement::ConcentrationUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::DistanceUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::MassUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::Measurement(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::QuantityUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::TemperatureUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::TimeUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::Unit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Measurement::VolumeUnit(3pm)	Class for the MAGE-OM API.
Bio::MAGE::NameValueType(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol(3pm)	Container module for classes in the MAGE package: Protocol.
Bio::MAGE::Protocol::Hardware(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::HardwareApplication(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::Parameter(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::Parameterizable(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::ParameterizableApplication(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::ParameterValue(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::Protocol(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::ProtocolApplication(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::Software(3pm)	Class for the MAGE-OM API.
Bio::MAGE::Protocol::SoftwareApplication(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType(3pm)	Container module for classes in the MAGE package: QuantitationType.
Bio::MAGE::QuantitationType::ConfidenceIndicator(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::DerivedSignal(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::Error(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::ExpectedValue(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::Failed(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::MeasuredSignal(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::PresentAbsent(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::PValue(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::QuantitationType(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::Ratio(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::SpecializedQuantitationType(3pm)	Class for the MAGE-OM API.
Bio::MAGE::QuantitationType::StandardQuantitationType(3pm)	Class for the MAGE-OM API.
Bio::MAGE::SQLUtils(3pm)	A module for exporting MAGE-OM objects to a database.
Bio::MAGE::Tools::MGEDOntologyClassEntry(3pm)	…
Bio::MAGE::Tools::MGEDOntologyEntry(3pm)	…
Bio::MAGE::Tools::MGEDOntologyHelper(3pm)	…
Bio::MAGE::Tools::MGEDOntologyPropertyEntry(3pm)	…
Bio::MAGE::XML::Handler(3pm)	…
Bio::MAGE::XML::Handler::ObjectHandler::SQL(3pm)	DESCRIPTION of Object.
Bio::MAGE::XML::Handler::ObjectHandlerI(3pm)	Abstract class for processing Bio::MAGE objects.
Bio::MAGE::XML::Reader(3pm)	A module for exporting MAGE-ML.
Bio::MAGE::XML::Writer(3pm)	A module for exporting MAGE-ML.
Bio::Map::Clone(3pm)	An central map object representing a clone.
Bio::Map::Contig(3pm)	A MapI implementation handling the contigs of a Physical Map (such as FPC).
Bio::Map::CytoMap(3pm)	A Bio::MapI compliant map implementation handling cytogenic bands.
Bio::Map::CytoMarker(3pm)	An object representing a marker.
Bio::Map::CytoPosition(3pm)	Marker class with cytogenetic band storing attributes.
Bio::Map::EntityI(3pm)	An Entity Interface.
Bio::Map::FPCMarker(3pm)	An central map object representing a marker.
Bio::Map::Gene(3pm)	An gene modelled as a mappable element.
Bio::Map::GeneMap(3pm)	A MapI implementation to represent the area around a gene.
Bio::Map::GenePosition(3pm)	A typed position, suitable for modelling the various.
Bio::Map::GeneRelative(3pm)	Represents being relative to named sub-regions of a.
Bio::Map::LinkageMap(3pm)	A representation of a genetic linkage map.
Bio::Map::LinkagePosition(3pm)	Create a Position for a Marker that will be placed on.
Bio::Map::MapI(3pm)	Interface for describing Map objects in bioperl.
Bio::Map::Mappable(3pm)	An object representing a generic map element that can have multiple locations in several.
Bio::Map::MappableI(3pm)	An object that can be placed in a map.
Bio::Map::Marker(3pm)	An central map object representing a generic marker that can have multiple location in.
Bio::Map::MarkerI(3pm)	Interface for basic marker functionality.
Bio::Map::Microsatellite(3pm)	An object representing a Microsatellite marker.
Bio::Map::OrderedPosition(3pm)	Abstracts the notion of a member of an ordered list of markers. Each marker.
Bio::Map::OrderedPositionWithDistance(3pm)	Abstracts the notion of a member of an ordered list of markers.
Bio::Map::Physical(3pm)	A class for handling a Physical Map (such as FPC).
Bio::Map::Position(3pm)	A single position of a Marker, or the range over which.
Bio::Map::PositionHandler(3pm)	A Position Handler Implementation.
Bio::Map::PositionHandlerI(3pm)	A Position Handler Interface.
Bio::Map::PositionI(3pm)	Abstracts the notion of a position having a value in the context of a marker and a Map.
Bio::Map::PositionWithSequence(3pm)	A position with a sequence.
Bio::Map::Prediction(3pm)	An object representing the predictions of something that can have multiple locations in.
Bio::Map::Relative(3pm)	Represents what a Position's coordiantes are relative to.
Bio::Map::RelativeI(3pm)	Interface for describing what a Position's coordiantes are.
Bio::Map::SimpleMap(3pm)	A MapI implementation handling the basics of a Map.
Bio::Map::TranscriptionFactor(3pm)	A transcription factor modelled as a mappable element.
Bio::MapIO(3pm)	A Map Factory object.
Bio::MapIO::fpc(3pm)	A FPC Map reader.
Bio::MapIO::mapmaker(3pm)	A Mapmaker Map reader.
Bio::Matrix::Generic(3pm)	A generic matrix implementation.
Bio::Matrix::IO(3pm)	A factory for Matrix parsing.
Bio::Matrix::IO::mlagan(3pm)	A parser for the mlagan substitution matrix.
Bio::Matrix::IO::phylip(3pm)	A parser for PHYLIP distance matricies.
Bio::Matrix::IO::scoring(3pm)	A parser for PAM/BLOSUM matricies.
Bio::Matrix::MatrixI(3pm)	An interface for describing a Matrix.
Bio::Matrix::Mlagan(3pm)	A generic matrix with mlagan fields.
Bio::Matrix::PhylipDist(3pm)	A Phylip Distance Matrix object.
Bio::Matrix::PSM::InstanceSite(3pm)	A PSM site occurance.
Bio::Matrix::PSM::InstanceSiteI(3pm)	InstanceSite interface, holds an instance of a PSM.
Bio::Matrix::PSM::IO(3pm)	PSM parser.
Bio::Matrix::PSM::IO::mast(3pm)	PSM mast parser implementation.
Bio::Matrix::PSM::IO::masta(3pm)	Motif fasta format parser.
Bio::Matrix::PSM::IO::meme(3pm)	PSM meme parser implementation.
Bio::Matrix::PSM::IO::psiblast(3pm)	PSM psiblast parser.
Bio::Matrix::PSM::IO::transfac(3pm)	PSM transfac parser.
Bio::Matrix::PSM::ProtMatrix(3pm)	SiteMatrixI implementation, holds a position scoring matrix (or position weight.
Bio::Matrix::PSM::ProtPsm(3pm)	Handle combination of site matricies.
Bio::Matrix::PSM::Psm(3pm)	Handle combination of site matricies.
Bio::Matrix::PSM::PsmHeader(3pm)	PSM mast parser implementation.
Bio::Matrix::PSM::PsmHeaderI(3pm)	Handles the header data from a PSM file.
Bio::Matrix::PSM::PsmI(3pm)	Abstract interface to handler of site matricies.
Bio::Matrix::PSM::SiteMatrix(3pm)	SiteMatrixI implementation, holds a position scoring matrix (or position weight.
Bio::Matrix::PSM::SiteMatrixI(3pm)	SiteMatrixI implementation, holds a position scoring matrix (or position.
Bio::Matrix::Scoring(3pm)	Object which can hold scoring matrix information.
Bio::MolEvol::CodonModel(3pm)	Codon Evolution Models.
Bio::Nexml::Factory(3pm)	A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents.
Bio::NexmlIO(3pm)	Stream handler for NeXML documents.
Bio::Ontology::DocumentRegistry(3pm)	Keep track of where to find ontologies. Allows lookups by name.
Bio::Ontology::GOterm(3pm)	Representation of GO terms.
Bio::Ontology::InterProTerm(3pm)	Implementation of InterProI term interface.
Bio::Ontology::OBOEngine(3pm)	An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium.
Bio::Ontology::OBOterm(3pm)	Representation of OBO terms.
Bio::Ontology::Ontology(3pm)	Standard implementation of an Ontology.
Bio::Ontology::OntologyEngineI(3pm)	Interface a minimal Ontology implementation should satisfy.
Bio::Ontology::OntologyI(3pm)	Interface for an ontology implementation.
Bio::Ontology::OntologyStore(3pm)	A repository of ontologies.
Bio::Ontology::Path(3pm)	A path for an ontology term graph.
Bio::Ontology::PathI(3pm)	Interface for a path between ontology terms.
Bio::Ontology::Relationship(3pm)	A relationship for an ontology.
Bio::Ontology::RelationshipFactory(3pm)	Instantiates a new Bio::Ontology::RelationshipI (or derived class).
Bio::Ontology::RelationshipI(3pm)	Interface for a relationship between ontology terms.
Bio::Ontology::RelationshipType(3pm)	A relationship type for an ontology.
Bio::Ontology::SimpleGOEngine::GraphAdaptor(3pm)	Graph adaptor for Bio::Ontology::SimpleGOEngine.
Bio::Ontology::SimpleOntologyEngine(3pm)	Implementation of OntologyEngineI interface.
Bio::Ontology::Term(3pm)	Implementation of the interface for ontology terms.
Bio::Ontology::TermFactory(3pm)	Instantiates a new Bio::Ontology::TermI (or derived class) through a factory.
Bio::Ontology::TermI(3pm)	Interface for ontology terms.
Bio::OntologyIO(3pm)	Parser factory for Ontology formats.
Bio::OntologyIO::dagflat(3pm)	A base class parser for GO flat-file type formats.
Bio::OntologyIO::goflat(3pm)	A parser for the Gene Ontology flat-file format.
Bio::OntologyIO::Handlers::BaseSAXHandler(3pm)	…
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler(3pm)	Parse an InterPro XML file and persist the resulting.
Bio::OntologyIO::Handlers::InterProHandler(3pm)	XML handler class for InterProParser.
Bio::OntologyIO::InterProParser(3pm)	Parser for InterPro xml files.
Bio::OntologyIO::obo(3pm)	A parser for OBO flat-file format from Gene Ontology Consortium.
Bio::OntologyIO::simplehierarchy(3pm)	A base class parser for simple hierarchy-by-indentation.
Bio::OntologyIO::soflat(3pm)	A parser for the Sequence Ontology flat-file format.
Bio::ParameterBaseI(3pm)	Simple interface class for any parameter-related data such as IDs, database name,.
Bio::Perl(3pm)	Functional access to BioPerl for people who don't know objects.
Bio::Phenotype::Correlate(3pm)	Representation of a correlating phenotype in a given species.
Bio::Phenotype::Measure(3pm)	Representation of context/value(-range)/unit triplets.
Bio::Phenotype::MeSH::Term(3pm)	A MeSH term.
Bio::Phenotype::MeSH::Twig(3pm)	Context for a MeSH term.
Bio::Phenotype::OMIM::MiniMIMentry(3pm)	Representation of a Mini MIM entry.
Bio::Phenotype::OMIM::OMIMentry(3pm)	Represents OMIM (Online Mendelian Inheritance in Man) database entries.
Bio::Phenotype::OMIM::OMIMentryAllelicVariant(3pm)	Representation of a allelic variant of the OMIM database.
Bio::Phenotype::OMIM::OMIMparser(3pm)	Parser for the OMIM database.
Bio::Phenotype::Phenotype(3pm)	A class for modeling phenotypes.
Bio::Phenotype::PhenotypeI(3pm)	An interface for classes modeling phenotypes.
Bio::PhyloNetwork(3pm)	Module to compute with Phylogenetic Networks.
Bio::PhyloNetwork::Factory(3pm)	Module to sequentially generate Phylogenetic Networks.
Bio::PhyloNetwork::FactoryX(3pm)	Module to sequentially generate Phylogenetic Networks.
Bio::PhyloNetwork::GraphViz(3pm)	Interface between PhyloNetwork and GraphViz.
Bio::PhyloNetwork::muVector(3pm)	Module to compute with vectors of arbitrary dimension.
Bio::PhyloNetwork::RandomFactory(3pm)	Module to generate random Phylogenetic Networks.
Bio::PhyloNetwork::TreeFactory(3pm)	Module to sequentially generate Phylogenetic Trees.
Bio::PhyloNetwork::TreeFactoryMulti(3pm)	Module to sequentially generate Phylogenetic Trees.
Bio::PhyloNetwork::TreeFactoryX(3pm)	Module to sequentially generate Phylogenetic Trees.
Bio::PopGen::Genotype(3pm)	An implementation of GenotypeI which is just an allele container.
Bio::PopGen::GenotypeI(3pm)	A marker and alleles for a specific individual.
Bio::PopGen::HtSNP(3pm)	…
Bio::PopGen::Individual(3pm)	An implementation of an Individual who has Genotype or Sequence Results.
Bio::PopGen::IndividualI(3pm)	An individual who has Genotype or Sequence Results.
Bio::PopGen::IO(3pm)	Input individual,marker,allele information.
Bio::PopGen::IO::csv(3pm)	…
Bio::PopGen::IO::hapmap(3pm)	A parser for HapMap output data.
Bio::PopGen::IO::phase(3pm)	A parser for Phase format data.
Bio::PopGen::IO::prettybase(3pm)	Extract individual allele data from PrettyBase format.
Bio::PopGen::Marker(3pm)	A genetic marker which one uses to generate genotypes.
Bio::PopGen::MarkerI(3pm)	A Population Genetic conceptual marker.
Bio::PopGen::PopStats(3pm)	A collection of methods for calculating statistics about a population or sets of.
Bio::PopGen::Population(3pm)	A population of individuals.
Bio::PopGen::PopulationI(3pm)	Interface for Populations.
Bio::PopGen::Simulation::Coalescent(3pm)	A Coalescent simulation factory.
Bio::PopGen::Simulation::GeneticDrift(3pm)	A simple genetic drift simulation.
Bio::PopGen::Statistics(3pm)	Population Genetics statistical tests.
Bio::PopGen::TagHaplotype(3pm)	Haplotype tag object.
Bio::PopGen::Utilities(3pm)	Utilities for working with PopGen data and objects.
Bio::PrimarySeq(3pm)	Bioperl lightweight sequence object.
Bio::PrimarySeqI(3pm)	Interface definition for a Bio::PrimarySeq.
Bio::PrimerDesigner(3pm)	Design PCR Primers using primer3 and epcr.
Bio::PrimerDesigner::epcr(3pm)	A class for accessing the epcr binary.
Bio::PrimerDesigner::ispcr(3pm)	A class for accessing the isPcr (in-silico PCR) binary.
Bio::PrimerDesigner::primer3(3pm)	An class for accessing primer3.
Bio::PrimerDesigner::Remote(3pm)	A class for remote access to Bio::PrimerDesigner.
Bio::PrimerDesigner::Result(3pm)	A class for handling primer design or validation results.
Bio::PrimerDesigner::Tables(3pm)	…
Bio::PullParserI(3pm)	A base module for fast 'pull' parsing.
Bio::Range(3pm)	Pure perl RangeI implementation.
Bio::RangeI(3pm)	Range interface.
Bio::Restriction::Analysis(3pm)	Cutting sequences with restriction enzymes.
Bio::Restriction::Enzyme(3pm)	A single restriction endonuclease (cuts DNA at specific locations).
Bio::Restriction::Enzyme::MultiCut(3pm)	A single restriction endonuclease.
Bio::Restriction::Enzyme::MultiSite(3pm)	A single restriction endonuclease.
Bio::Restriction::EnzymeCollection(3pm)	Set of restriction endonucleases.
Bio::Restriction::EnzymeI(3pm)	Interface class for restriction endonuclease.
Bio::Restriction::IO(3pm)	Handler for sequence variation IO Formats.
Bio::Restriction::IO::bairoch(3pm)	Bairoch enzyme set.
Bio::Restriction::IO::base(3pm)	Base enzyme set.
Bio::Restriction::IO::itype2(3pm)	Itype2 enzyme set.
Bio::Restriction::IO::prototype(3pm)	Prototype enzyme set.
Bio::Restriction::IO::withrefm(3pm)	Withrefm enzyme set.
Bio::Roary(3pm)	Create a pan genome.
Bio::Roary::AccessoryBinaryFasta(3pm)	Output a FASTA file which represents the binary presence and absence of.
Bio::Roary::AccessoryClustering(3pm)	Take an a clusters file from CD-hit and the fasta file and output a fasta.
Bio::Roary::AnalyseGroups(3pm)	Take in a groups file and the original FASTA files and create plots and stats.
Bio::Roary::AnnotateGroups(3pm)	Take in a group file and assosiated GFF files for the isolates and update the.
Bio::Roary::AssemblyStatistics(3pm)	Given a spreadsheet of gene presence and absence calculate some statistics.
Bio::Roary::BedFromGFFRole(3pm)	A role to create a bed file from a gff.
Bio::Roary::ChunkFastaFile(3pm)	Take in a FASTA file and chunk it up into smaller pieces.
Bio::Roary::ClustersRole(3pm)	A role to read a clusters file from CD hit.
Bio::Roary::CombinedProteome(3pm)	Take in multiple FASTA sequences containing proteomes and concat them together.
Bio::Roary::CommandLine::AssemblyStatistics(3pm)	Given a spreadsheet of gene presence and absence calculate some.
Bio::Roary::CommandLine::Common(3pm)	Common command line settings.
Bio::Roary::CommandLine::CreatePanGenome(3pm)	Take in FASTA files of proteins and cluster them.
Bio::Roary::CommandLine::ExtractProteomeFromGff(3pm)	Take in GFF files and output the proteome.
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides(3pm)	Take in a multifasta file of nucleotides, convert to.
Bio::Roary::CommandLine::IterativeCdhit(3pm)	Iteratively run cdhit.
Bio::Roary::CommandLine::ParallelAllAgainstAllBlastp(3pm)	Take in a FASTA file of proteins and blast against.
Bio::Roary::CommandLine::QueryRoary(3pm)	Take in a groups file and the protein fasta files and output selected.
Bio::Roary::CommandLine::Roary(3pm)	Take in FASTA files of proteins and cluster them.
Bio::Roary::CommandLine::RoaryCoreAlignment(3pm)	Take in the group statistics spreadsheet and the location of the.
Bio::Roary::CommandLine::RoaryPostAnalysis(3pm)	Perform the post analysis on the pan genome.
Bio::Roary::CommandLine::RoaryReorderSpreadsheet(3pm)	Take in a tree and a spreadsheet and output a reordered.
Bio::Roary::CommandLine::TransferAnnotationToGroups(3pm)	Take in a groups file and a set of GFF files and.
Bio::Roary::ContigsToGeneIDsFromGFF(3pm)	Parse a GFF and efficiently and extract ordered gene ids on each contig.
Bio::Roary::Exceptions(3pm)	Exceptions for input data.
Bio::Roary::External::Blastp(3pm)	Wrapper around NCBIs blastp command.
Bio::Roary::External::Cdhit(3pm)	Wrapper to run cd-hit.
Bio::Roary::External::CheckTools(3pm)	Check external executables are available and are the correct version.
Bio::Roary::External::Fasttree(3pm)	Wrapper to run Fasttree.
Bio::Roary::External::GeneAlignmentFromNucleotides(3pm)	Take in multi-FASTA files of nucleotides and align each.
Bio::Roary::External::IterativeCdhit(3pm)	Iteratively run CDhit.
Bio::Roary::External::Mafft(3pm)	Wrapper to run mafft.
Bio::Roary::External::Makeblastdb(3pm)	Wrapper around NCBIs makeblastdb command.
Bio::Roary::External::Mcl(3pm)	Wrapper around MCL which takes in blast results and outputs clustered results.
Bio::Roary::External::PostAnalysis(3pm)	Perform the post analysis.
Bio::Roary::External::Prank(3pm)	Wrapper to run prank.
Bio::Roary::ExtractCoreGenesFromSpreadsheet(3pm)	Take in a spreadsheet produced by the pipeline and identify the.
Bio::Roary::ExtractProteomeFromGFF(3pm)	Take in a GFF file and create protein sequences in FASTA format.
Bio::Roary::ExtractProteomeFromGFFs(3pm)	Take in GFF files and create protein sequences in FASTA format.
Bio::Roary::FilterFullClusters(3pm)	Take an a clusters file from CD-hit and the fasta file and output a fasta.
Bio::Roary::FilterUnknownsFromFasta(3pm)	Take in fasta files, remove sequences with too many unknowns and return.
Bio::Roary::GeneNamesFromGFF(3pm)	Parse a GFF and efficiently extract ID -> Gene Name.
Bio::Roary::GroupLabels(3pm)	Add labels to the groups.
Bio::Roary::GroupStatistics(3pm)	Add labels to the groups.
Bio::Roary::InflateClusters(3pm)	Take the clusters file from cd-hit and use it to inflate the output of MCL.
Bio::Roary::IterativeCdhit(3pm)	Run CDhit iteratively with reducing thresholds, removing full clusters each time.
Bio::Roary::JobRunner::Local(3pm)	Execute a set of commands locally.
Bio::Roary::JobRunner::Parallel(3pm)	Use GNU Parallel.
Bio::Roary::JobRunner::Role(3pm)	A role to add job runner functionality.
Bio::Roary::LookupGeneFiles(3pm)	Take in an ordering of genes and a directory and return an ordered list of file.
Bio::Roary::MergeMultifastaAlignments(3pm)	Merge multifasta alignment files with equal numbers of sequences.
Bio::Roary::OrderGenes(3pm)	Take in GFF files and create a matrix of what genes are beside what other genes.
Bio::Roary::Output::BlastIdentityFrequency(3pm)	Take in blast results and find the percentage identity graph.
Bio::Roary::Output::CoreGeneAlignmentCoordinatesEMBL(3pm)	Create an embl file for the header with locations of.
Bio::Roary::Output::DifferenceBetweenSets(3pm)	Given two sets of isolates and a group file, output whats unique.
Bio::Roary::Output::EmblGroups(3pm)	Create a tab/embl file with the features for drawing pretty pictures.
Bio::Roary::Output::EMBLHeaderCommon(3pm)	A role containing some common methods for embl header files.
Bio::Roary::Output::GroupMultifasta(3pm)	Take in a group and create a multifasta file.
Bio::Roary::Output::GroupsMultifastaNucleotide(3pm)	Take in a GFF files and a groups file and output one.
Bio::Roary::Output::GroupsMultifastaProtein(3pm)	Take a multifasta nucleotide file and output it as proteins.
Bio::Roary::Output::GroupsMultifastas(3pm)	Take in a list of groups and create multifastas files for each group.
Bio::Roary::Output::GroupsMultifastasNucleotide(3pm)	Take in a set of GFF files and a groups file and output one.
Bio::Roary::Output::NumberOfGroups(3pm)	Create raw output files of group counts for turning into plots.
Bio::Roary::Output::QueryGroups(3pm)	Output the groups of the union of a set of input isolates.
Bio::Roary::ParallelAllAgainstAllBlast(3pm)	Run all against all blast in parallel.
Bio::Roary::ParseGFFAnnotationRole(3pm)	A role for parsing a gff file efficiently.
Bio::Roary::PostAnalysis(3pm)	Post analysis of pan genomes.
Bio::Roary::PrepareInputFiles(3pm)	Take in a mixture of FASTA and GFF input files and output FASTA proteomes only.
Bio::Roary::PresenceAbsenceMatrix(3pm)	Create a matrix with presence and absence.
Bio::Roary::QC::Report(3pm)	Generate a report based on kraken output.
Bio::Roary::ReformatInputGFFs(3pm)	Take in gff files and add suffix where a gene id is seen twice.
Bio::Roary::ReorderSpreadsheet(3pm)	Take in a tree file and a spreadsheet and output a spreadsheet with reordered.
Bio::Roary::SampleOrder(3pm)	Take in a tree file and return an ordering of the samples.
Bio::Roary::SequenceLengths(3pm)	Take in a fasta file and create a hash with the length of each sequence.
Bio::Roary::SortFasta(3pm)	Sort a fasta file by name.
Bio::Roary::SplitGroups(3pm)	Split groups.
Bio::Roary::SpreadsheetRole(3pm)	Read and write a spreadsheet.
Bio::Root::Build(3pm)	…
Bio::Root::Exception(3pm)	…
Bio::Root::HTTPget(3pm)	Module for fallback HTTP get operations when LWP:: is unavailable.
Bio::Root::IO(3pm)	…
Bio::Root::Root(3pm)	…
Bio::Root::RootI(3pm)	…
Bio::Root::Storable(3pm)	…
Bio::Root::Test(3pm)	…
Bio::Root::Utilities(3pm)	…
Bio::Root::Version(3pm)	…
Bio::SCF(3pm)	Perl extension for reading and writing SCF sequence files.
Bio::Search::BlastStatistics(3pm)	An object for Blast statistics.
Bio::Search::BlastUtils(3pm)	Utility functions for Bio::Search:: BLAST objects.
Bio::Search::DatabaseI(3pm)	Interface for a database used in a sequence search.
Bio::Search::GenericDatabase(3pm)	Generic implementation of Bio::Search::DatabaseI.
Bio::Search::GenericStatistics(3pm)	An object for statistics.
Bio::Search::Hit::BlastHit(3pm)	Blast-specific subclass of Bio::Search::Hit::GenericHit.
Bio::Search::Hit::BlastPullHit(3pm)	A parser and hit object for BLASTN hits.
Bio::Search::Hit::Fasta(3pm)	Hit object specific for Fasta-generated hits.
Bio::Search::Hit::GenericHit(3pm)	A generic implementation of the Bio::Search::Hit::HitI interface.
Bio::Search::Hit::HitFactory(3pm)	A factory to create Bio::Search::Hit::HitI objects.
Bio::Search::Hit::HitI(3pm)	Interface for a hit in a similarity search result.
Bio::Search::Hit::hmmer3Hit(3pm)	DESCRIPTION of Object.
Bio::Search::Hit::HMMERHit(3pm)	A Hit module for HMMER hits.
Bio::Search::Hit::HmmpfamHit(3pm)	A parser and hit object for hmmpfam hits.
Bio::Search::Hit::ModelHit(3pm)	A model-based implementation of the Bio::Search::Hit::HitI interface.
Bio::Search::Hit::PsiBlastHit(3pm)	Bioperl BLAST Hit object.
Bio::Search::Hit::PullHitI(3pm)	Bio::Search::Hit::HitI interface for pull parsers.
Bio::Search::HSP::BlastHSP(3pm)	Bioperl BLAST High-Scoring Pair object.
Bio::Search::HSP::BlastPullHSP(3pm)	A parser and HSP object for BlastN hsps.
Bio::Search::HSP::FastaHSP(3pm)	HSP object for FASTA specific data.
Bio::Search::HSP::GenericHSP(3pm)	A "Generic" implementation of a High Scoring Pair.
Bio::Search::HSP::HMMERHSP(3pm)	A HSP object for HMMER results.
Bio::Search::HSP::HmmpfamHSP(3pm)	A parser and HSP object for hmmpfam hsps.
Bio::Search::HSP::HSPFactory(3pm)	A factory to create Bio::Search::HSP::HSPI objects.
Bio::Search::HSP::HSPI(3pm)	Interface for a High Scoring Pair in a similarity search result.
Bio::Search::HSP::ModelHSP(3pm)	A HSP object for model-based searches.
Bio::Search::HSP::PsiBlastHSP(3pm)	Bioperl BLAST High-Scoring Pair object.
Bio::Search::HSP::PSLHSP(3pm)	A HSP for PSL output.
Bio::Search::HSP::PullHSPI(3pm)	Bio::Search::HSP::HSPI interface for pull parsers.
Bio::Search::HSP::WABAHSP(3pm)	HSP object suitable for describing WABA alignments.
Bio::Search::Iteration::GenericIteration(3pm)	A generic implementation of the Bio::Search::Iteration::IterationI.
Bio::Search::Iteration::IterationI(3pm)	Abstract interface to an iteration from an iterated search result, such.
Bio::Search::Processor(3pm)	DESCRIPTION of Object.
Bio::Search::Result::BlastPullResult(3pm)	A parser and result object for BLASTN.
Bio::Search::Result::BlastResult(3pm)	Blast-specific subclass of Bio::Search::Result::GenericResult.
Bio::Search::Result::CrossMatchResult(3pm)	CrossMatch-specific subclass of Bio::Search::Result::GenericResult.
Bio::Search::Result::GenericResult(3pm)	Generic Implementation of Bio::Search::Result::ResultI interface.
Bio::Search::Result::hmmer3Result(3pm)	DESCRIPTION of Object.
Bio::Search::Result::HMMERResult(3pm)	A Result object for HMMER results.
Bio::Search::Result::HmmpfamResult(3pm)	A parser and result object for hmmpfam.
Bio::Search::Result::PullResultI(3pm)	Bio::Search::Result::ResultI interface for.
Bio::Search::Result::ResultFactory(3pm)	A factory to create Bio::Search::Result::ResultI objects.
Bio::Search::Result::ResultI(3pm)	Abstract interface to Search Result objects.
Bio::Search::Result::WABAResult(3pm)	Result object for WABA alignment output.
Bio::Search::SearchUtils(3pm)	Utility functions for Bio::Search:: objects.
Bio::Search::StatisticsI(3pm)	A Base object for statistics.
Bio::Search::Tiling::MapTileUtils(3pm)	Utilities for manipulating closed intervals for an HSP tiling algorithm.
Bio::Search::Tiling::MapTiling(3pm)	An implementation of an HSP tiling algorithm, with methods to obtain.
Bio::Search::Tiling::TilingI(3pm)	Abstract interface for an HSP tiling module.
Bio::SearchDist(3pm)	A perl wrapper around Sean Eddy's histogram object.
Bio::SearchIO(3pm)	Driver for parsing Sequence Database Searches (BLAST, FASTA, ...).
Bio::SearchIO::axt(3pm)	A parser for axt format reports.
Bio::SearchIO::blast(3pm)	Event generator for event based parsing of blast reports.
Bio::SearchIO::blast_pull(3pm)	A parser for BLAST output.
Bio::SearchIO::blasttable(3pm)	Driver module for SearchIO for parsing NCBI -m 8/9 format.
Bio::SearchIO::blastxml(3pm)	A SearchIO implementation of NCBI Blast XML parsing.
Bio::SearchIO::cross_match(3pm)	CrossMatch-specific subclass of Bio::SearchIO.
Bio::SearchIO::erpin(3pm)	SearchIO-based ERPIN parser.
Bio::SearchIO::EventHandlerI(3pm)	An abstract Event Handler for Search Result parsing.
Bio::SearchIO::exonerate(3pm)	Parser for Exonerate.
Bio::SearchIO::fasta(3pm)	A SearchIO parser for FASTA results.
Bio::SearchIO::FastHitEventBuilder(3pm)	Event Handler for SearchIO events.
Bio::SearchIO::gmap_f9(3pm)	Event generator for parsing gmap reports (Z format).
Bio::SearchIO::hmmer(3pm)	A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam).
Bio::SearchIO::hmmer2(3pm)	A parser for HMMER output (hmmpfam, hmmsearch).
Bio::SearchIO::hmmer3(3pm)	…
Bio::SearchIO::hmmer_pull(3pm)	A parser for HMMER output.
Bio::SearchIO::infernal(3pm)	SearchIO-based Infernal parser.
Bio::SearchIO::IteratedSearchResultEventBuilder(3pm)	Event Handler for SearchIO events.
Bio::SearchIO::megablast(3pm)	A driver module for Bio::SearchIO to parse megablast reports (format 0).
Bio::SearchIO::psl(3pm)	A parser for PSL output (UCSC).
Bio::SearchIO::rnamotif(3pm)	SearchIO-based RNAMotif parser.
Bio::SearchIO::SearchResultEventBuilder(3pm)	Event Handler for SearchIO events.
Bio::SearchIO::SearchWriterI(3pm)	Interface for outputting parsed Search results.
Bio::SearchIO::sim4(3pm)	Parser for Sim4 alignments.
Bio::SearchIO::waba(3pm)	SearchIO parser for Jim Kent WABA program alignment output.
Bio::SearchIO::wise(3pm)	Parsing of wise output as alignments.
Bio::SearchIO::Writer::BSMLResultWriter(3pm)	BSML output writer.
Bio::SearchIO::Writer::GbrowseGFF(3pm)	Interface for outputting parsed search results in Gbrowse GFF format.
Bio::SearchIO::Writer::HitTableWriter(3pm)	Tab-delimited data for Bio::Search::Hit::HitI objects.
Bio::SearchIO::Writer::HSPTableWriter(3pm)	Tab-delimited data for Bio::Search::HSP::HSPI objects.
Bio::SearchIO::Writer::HTMLResultWriter(3pm)	Write a Bio::Search::ResultI in HTML.
Bio::SearchIO::Writer::ResultTableWriter(3pm)	Outputs tab-delimited data for each Bio::Search::Result::ResultI.
Bio::SearchIO::Writer::TextResultWriter(3pm)	Object to implement writing a Bio::Search::ResultI in Text.
Bio::SearchIO::XML::BlastHandler(3pm)	XML Handler for NCBI Blast XML parsing.
Bio::SearchIO::XML::PsiBlastHandler(3pm)	XML Handler for NCBI Blast PSIBLAST XML parsing.
Bio::Seq(3pm)	Sequence object, with features.
Bio::Seq::BaseSeqProcessor(3pm)	Base implementation for a SequenceProcessor.
Bio::Seq::EncodedSeq(3pm)	Subtype of Bio::LocatableSeq to store DNA that encodes a protein.
Bio::Seq::LargeLocatableSeq(3pm)	LocatableSeq object that stores sequence as files in the tempdir.
Bio::Seq::LargePrimarySeq(3pm)	PrimarySeq object that stores sequence as files in the tempdir (as found by.
Bio::Seq::LargeSeq(3pm)	SeqI compliant object that stores sequence as files in /tmp.
Bio::Seq::LargeSeqI(3pm)	Interface class for sequences that cache their residues in a temporary file.
Bio::Seq::Meta(3pm)	Generic superclass for sequence objects with residue-based meta information.
Bio::Seq::Meta::Array(3pm)	Array-based generic implementation of a sequence class with residue-based meta.
Bio::Seq::MetaI(3pm)	Interface for sequence objects with residue-based meta information.
Bio::Seq::PrimaryQual(3pm)	Bioperl lightweight Quality Object.
Bio::Seq::PrimedSeq(3pm)	A sequence and a pair of primers matching on it.
Bio::Seq::QualI(3pm)	Interface definition for a Bio::Seq::Qual.
Bio::Seq::Quality(3pm)	Implementation of sequence with residue quality.
Bio::Seq::RichSeq(3pm)	Module implementing a sequence created from a rich sequence database entry.
Bio::Seq::RichSeqI(3pm)	Interface for sequences from rich data sources, mostly databases.
Bio::Seq::SeqBuilder(3pm)	Configurable object builder for sequence stream parsers.
Bio::Seq::SeqFactory(3pm)	Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory.
Bio::Seq::SeqFastaSpeedFactory(3pm)	Rapid creation of Bio::Seq objects through a factory.
Bio::Seq::SequenceTrace(3pm)	Bioperl object packaging a sequence with its trace.
Bio::Seq::SeqWithQuality(3pm)	Bioperl object packaging a sequence with its quality. Deprecated class, use.
Bio::Seq::SimulatedRead(3pm)	Read with sequencing errors taken from a reference sequence.
Bio::Seq::TraceI(3pm)	Interface definition for a Bio::Seq::Trace.
Bio::SeqAnalysisParserI(3pm)	Sequence analysis output parser interface.
Bio::SeqEvolution::DNAPoint(3pm)	Evolve a sequence by point mutations.
Bio::SeqEvolution::EvolutionI(3pm)	The interface for evolving sequences.
Bio::SeqEvolution::Factory(3pm)	Factory object to instantiate sequence evolving classes.
Bio::SeqFeature::Amplicon(3pm)	Amplicon feature.
Bio::SeqFeature::AnnotationAdaptor(3pm)	Integrates SeqFeatureIs annotation.
Bio::SeqFeature::Collection(3pm)	A container class for SeqFeatures suitable for performing operations such as.
Bio::SeqFeature::CollectionI(3pm)	An interface for a collection of SeqFeatureI objects.
Bio::SeqFeature::Computation(3pm)	Computation SeqFeature.
Bio::SeqFeature::FeaturePair(3pm)	Hold pair feature information e.g. blast hits.
Bio::SeqFeature::Gene::Exon(3pm)	A feature representing an exon.
Bio::SeqFeature::Gene::ExonI(3pm)	Interface for a feature representing an exon.
Bio::SeqFeature::Gene::GeneStructure(3pm)	A feature representing an arbitrarily complex structure of a gene.
Bio::SeqFeature::Gene::GeneStructureI(3pm)	A feature representing an arbitrarily.
Bio::SeqFeature::Gene::Intron(3pm)	An intron feature.
Bio::SeqFeature::Gene::NC_Feature(3pm)	Superclass for non-coding features.
Bio::SeqFeature::Gene::Poly_A_site(3pm)	Poly A feature.
Bio::SeqFeature::Gene::Promoter(3pm)	Describes a promoter.
Bio::SeqFeature::Gene::Transcript(3pm)	A feature representing a transcript.
Bio::SeqFeature::Gene::TranscriptI(3pm)	Interface for a feature representing a.
Bio::SeqFeature::Gene::UTR(3pm)	A feature representing an untranslated region.
Bio::SeqFeature::Generic(3pm)	Generic SeqFeature.
Bio::SeqFeature::Lite(3pm)	Lightweight Bio::SeqFeatureI class.
Bio::SeqFeature::PositionProxy(3pm)	Handle features when truncation/revcom sequences span a feature.
Bio::SeqFeature::Primer(3pm)	Primer Generic SeqFeature.
Bio::SeqFeature::Similarity(3pm)	A sequence feature based on similarity.
Bio::SeqFeature::SimilarityPair(3pm)	Sequence feature based on the similarity.
Bio::SeqFeature::SiRNA::Oligo(3pm)	Perl object for small inhibitory RNAs.
Bio::SeqFeature::SiRNA::Pair(3pm)	Perl object for small inhibitory RNA (SiRNA) oligo pairs.
Bio::SeqFeature::SubSeq(3pm)	Feature representing a subsequence.
Bio::SeqFeature::Tools::FeatureNamer(3pm)	Generates unique persistent names for features.
Bio::SeqFeature::Tools::IDHandler(3pm)	Maps $seq_feature->primary_tag.
Bio::SeqFeature::Tools::TypeMapper(3pm)	Maps $seq_feature->primary_tag.
Bio::SeqFeature::Tools::Unflattener(3pm)	Turns flat list of genbank-sourced features into a nested SeqFeatureI.
Bio::SeqFeature::TypedSeqFeatureI(3pm)	A strongly typed SeqFeature.
Bio::SeqFeatureI(3pm)	Abstract interface of a Sequence Feature.
Bio::SeqI(3pm)	[Developers] Abstract Interface of Sequence (with features).
Bio::SeqIO(3pm)	Handler for SeqIO Formats.
Bio::SeqIO::abi(3pm)	Abi trace sequence input/output stream.
Bio::SeqIO::ace(3pm)	Ace sequence input/output stream.
Bio::SeqIO::agave(3pm)	AGAVE sequence output stream.
Bio::SeqIO::alf(3pm)	Alf trace sequence input/output stream.
Bio::SeqIO::asciitree(3pm)	Asciitree sequence input/output stream.
Bio::SeqIO::bsml(3pm)	BSML sequence input/output stream.
Bio::SeqIO::bsml_sax(3pm)	BSML sequence input/output stream using SAX.
Bio::SeqIO::chadoxml(3pm)	Chadoxml sequence output stream.
Bio::SeqIO::chaos(3pm)	Chaos sequence input/output stream.
Bio::SeqIO::chaosxml(3pm)	Chaosxml sequence input/output stream.
Bio::SeqIO::ctf(3pm)	Ctf trace sequence input/output stream.
Bio::SeqIO::embl(3pm)	EMBL sequence input/output stream.
Bio::SeqIO::embldriver(3pm)	EMBL sequence input/output stream.
Bio::SeqIO::entrezgene(3pm)	Entrez Gene ASN1 parser.
Bio::SeqIO::excel(3pm)	Sequence input/output stream from a.
Bio::SeqIO::exp(3pm)	Exp trace sequence input/output stream.
Bio::SeqIO::fasta(3pm)	Fasta sequence input/output stream.
Bio::SeqIO::fastq(3pm)	Fastq sequence input/output stream.
Bio::SeqIO::flybase_chadoxml(3pm)	FlyBase variant of chadoxml with sequence output stream.
Bio::SeqIO::FTHelper(3pm)	Helper class for EMBL/Genbank feature tables.
Bio::SeqIO::game(3pm)	…
Bio::SeqIO::game::featHandler(3pm)	…
Bio::SeqIO::game::gameHandler(3pm)	…
Bio::SeqIO::game::gameSubs(3pm)	…
Bio::SeqIO::game::gameWriter(3pm)	…
Bio::SeqIO::game::seqHandler(3pm)	…
Bio::SeqIO::gbdriver(3pm)	GenBank handler-based push parser.
Bio::SeqIO::gbxml(3pm)	GenBank sequence input/output stream using SAX.
Bio::SeqIO::gcg(3pm)	GCG sequence input/output stream.
Bio::SeqIO::genbank(3pm)	GenBank sequence input/output stream.
Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)	Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and.
Bio::SeqIO::interpro(3pm)	InterProScan XML input/output stream.
Bio::SeqIO::kegg(3pm)	KEGG sequence input/output stream.
Bio::SeqIO::largefasta(3pm)	Method i/o on very large fasta sequence files.
Bio::SeqIO::lasergene(3pm)	Lasergene sequence file input/output stream.
Bio::SeqIO::locuslink(3pm)	LocusLink input/output stream.
Bio::SeqIO::mbsout(3pm)	Input stream for output by Teshima et al.'s mbs.
Bio::SeqIO::metafasta(3pm)	Metafasta sequence input/output stream.
Bio::SeqIO::msout(3pm)	Input stream for output by Hudson's ms.
Bio::SeqIO::MultiFile(3pm)	Treating a set of files as a single input stream.
Bio::SeqIO::nexml(3pm)	NeXML sequence input/output stream.
Bio::SeqIO::phd(3pm)	Phd file input/output stream.
Bio::SeqIO::pir(3pm)	PIR sequence input/output stream.
Bio::SeqIO::pln(3pm)	Pln trace sequence input/output stream.
Bio::SeqIO::qual(3pm)	.qual file input/output stream.
Bio::SeqIO::raw(3pm)	Raw sequence file input/output stream.
Bio::SeqIO::scf(3pm)	.scf file input/output stream.
Bio::SeqIO::seqxml(3pm)	SeqXML sequence input/output stream.
Bio::SeqIO::strider(3pm)	DNA strider sequence input/output stream.
Bio::SeqIO::swiss(3pm)	Swissprot sequence input/output stream.
Bio::SeqIO::swissdriver(3pm)	SwissProt/UniProt handler-based push parser.
Bio::SeqIO::tab(3pm)	Nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n".
Bio::SeqIO::table(3pm)	Sequence input/output stream from a delimited table.
Bio::SeqIO::tigr(3pm)	TIGR XML sequence input/output stream.
Bio::SeqIO::tigrxml(3pm)	Parse TIGR (new) XML.
Bio::SeqIO::tinyseq(3pm)	Reading/writing sequences in NCBI TinySeq format.
Bio::SeqIO::tinyseq::tinyseqHandler(3pm)	XML event handlers to support NCBI TinySeq XML parsing.
Bio::SeqIO::ztr(3pm)	Ztr trace sequence input/output stream.
Bio::SeqUtils(3pm)	Additional methods for PrimarySeq objects.
Bio::SimpleAlign(3pm)	Multiple alignments held as a set of sequences.
Bio::SimpleAnalysisI(3pm)	A simple interface to any (local or remote) analysis tool.
Bio::Species(3pm)	Generic species object.
Bio::Structure::Atom(3pm)	Bioperl structure Object, describes an Atom.
Bio::Structure::Chain(3pm)	Bioperl structure Object, describes a chain.
Bio::Structure::Entry(3pm)	Bioperl structure Object, describes the whole entry.
Bio::Structure::IO(3pm)	Handler for Structure Formats.
Bio::Structure::IO::pdb(3pm)	PDB input/output stream.
Bio::Structure::Model(3pm)	Bioperl structure Object, describes a Model.
Bio::Structure::Residue(3pm)	Bioperl structure Object, describes a Residue.
Bio::Structure::SecStr::DSSP::Res(3pm)	Module for parsing/accessing dssp output.
Bio::Structure::SecStr::STRIDE::Res(3pm)	Module for parsing/accessing stride output.
Bio::Structure::StructureI(3pm)	Abstract Interface for a Structure objects.
Bio::Symbol::Alphabet(3pm)	BSANE/BioCORBA compliant symbol list alphabet.
Bio::Symbol::AlphabetI(3pm)	A Symbol Alphabet.
Bio::Symbol::DNAAlphabet(3pm)	A ready made DNA alphabet.
Bio::Symbol::ProteinAlphabet(3pm)	A ready made Protein alphabet.
Bio::Symbol::Symbol(3pm)	A biological symbol.
Bio::Symbol::SymbolI(3pm)	Interface for a Symbol.
Bio::Taxon(3pm)	A node in a represented taxonomy.
Bio::Taxonomy(3pm)	Representing Taxonomy.
Bio::Taxonomy::FactoryI(3pm)	Interface to define how to access NCBI Taxonoy.
Bio::Taxonomy::Node(3pm)	A node in a represented taxonomy.
Bio::Taxonomy::Taxon(3pm)	Generic Taxonomic Entity object.
Bio::Taxonomy::Tree(3pm)	An Organism Level Implementation of TreeI interface.
Bio::Tools::AlignFactory(3pm)	Base object for alignment factories.
Bio::Tools::Alignment::Consed(3pm)	A module to work with objects from consed .ace files.
Bio::Tools::Alignment::Trim(3pm)	A kludge to do specialized trimming of sequence based on quality.
Bio::Tools::AmpliconSearch(3pm)	Find amplicons in a template using degenerate PCR primers.
Bio::Tools::Analysis::DNA::ESEfinder(3pm)	A wrapper around ESEfinder server.
Bio::Tools::Analysis::Protein::Domcut(3pm)	A wrapper around Domcut server.
Bio::Tools::Analysis::Protein::ELM(3pm)	A wrapper around the ELM server which predicts short functional motifs on.
Bio::Tools::Analysis::Protein::GOR4(3pm)	A wrapper around GOR4 protein secondary structure prediction server.
Bio::Tools::Analysis::Protein::HNN(3pm)	A wrapper around the HNN protein secondary structure prediction server.
Bio::Tools::Analysis::Protein::Mitoprot(3pm)	A wrapper around Mitoprot server.
Bio::Tools::Analysis::Protein::NetPhos(3pm)	A wrapper around NetPhos server.
Bio::Tools::Analysis::Protein::Scansite(3pm)	A wrapper around the Scansite server.
Bio::Tools::Analysis::Protein::Sopma(3pm)	A wrapper around the Sopma protein secondary structure prediction.
Bio::Tools::Analysis::SimpleAnalysisBase(3pm)	Abstract superclass for SimpleAnalysis implementations.
Bio::Tools::AnalysisResult(3pm)	Base class for analysis result objects and parsers.
Bio::Tools::Blat(3pm)	Parser for Blat program.
Bio::Tools::CodonTable(3pm)	Codon table object.
Bio::Tools::Coil(3pm)	Parser for Coil output.
Bio::Tools::dpAlign(3pm)	Perl extension to do pairwise dynamic programming sequence alignment.
Bio::Tools::ECnumber(3pm)	Representation of EC numbers (Enzyme Classification).
Bio::Tools::EMBOSS::Palindrome(3pm)	Parse EMBOSS palindrome output.
Bio::Tools::EPCR(3pm)	Parse ePCR output and make features.
Bio::Tools::Eponine(3pm)	Results of one Eponine run.
Bio::Tools::ERPIN(3pm)	A parser for ERPIN output.
Bio::Tools::Est2Genome(3pm)	Parse est2genome output, makes simple Bio::SeqFeature::Generic objects.
Bio::Tools::ESTScan(3pm)	Results of one ESTScan run.
Bio::Tools::Fgenesh(3pm)	Parse results of one Fgenesh run.
Bio::Tools::FootPrinter(3pm)	Write sequence features in FootPrinter format.
Bio::Tools::Gel(3pm)	Calculates relative electrophoretic migration distances.
Bio::Tools::Geneid(3pm)	Results of one geneid run.
Bio::Tools::Genemark(3pm)	Results of one Genemark run.
Bio::Tools::Genewise(3pm)	Results of one Genewise run.
Bio::Tools::Genomewise(3pm)	Results of one Genomewise run.
Bio::Tools::Genscan(3pm)	Results of one Genscan run.
Bio::Tools::GFF(3pm)	A Bio::SeqAnalysisParserI compliant GFF format parser.
Bio::Tools::Glimmer(3pm)	Parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene.
Bio::Tools::Grail(3pm)	Results of one Grail run.
Bio::Tools::GuessSeqFormat(3pm)	Module for determining the sequence format of the contents of a file, a string,.
Bio::Tools::HMMER::Domain(3pm)	One particular domain hit from HMMER.
Bio::Tools::HMMER::Results(3pm)	Object representing HMMER output results.
Bio::Tools::HMMER::Set(3pm)	Set of identical domains from HMMER matches.
Bio::Tools::Hmmpfam(3pm)	Parser for Hmmpfam program.
Bio::Tools::Infernal(3pm)	A parser for Infernal output.
Bio::Tools::ipcress(3pm)	Parse ipcress output and make features.
Bio::Tools::isPcr(3pm)	Parse isPcr output and make features.
Bio::Tools::IUPAC(3pm)	Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence.
Bio::Tools::Lucy(3pm)	Object for analyzing the output from Lucy,.
Bio::Tools::Match(3pm)	Parses output from Transfac's match(TM).
Bio::Tools::MZEF(3pm)	Results of one MZEF run.
Bio::Tools::OddCodes(3pm)	Object holding alternative alphabet coding for one protein sequence.
Bio::Tools::Phylo::Gerp(3pm)	Parses output from GERP.
Bio::Tools::Phylo::Gumby(3pm)	Parses output from gumby.
Bio::Tools::Phylo::Molphy(3pm)	Parser for Molphy output.
Bio::Tools::Phylo::Molphy::Result(3pm)	Container for data parsed from a ProtML run.
Bio::Tools::Phylo::PAML(3pm)	Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00.
Bio::Tools::Phylo::PAML::Codeml(3pm)	Parses output from the PAML program codeml.
Bio::Tools::Phylo::PAML::ModelResult(3pm)	A container for NSSite Model Result from PAML.
Bio::Tools::Phylo::PAML::Result(3pm)	A PAML result set object.
Bio::Tools::Phylo::Phylip::ProtDist(3pm)	Parser for ProtDist output.
Bio::Tools::pICalculator(3pm)	Calculate the isoelectric point of a protein.
Bio::Tools::Prediction::Exon(3pm)	A predicted exon feature.
Bio::Tools::Prediction::Gene(3pm)	A predicted gene structure feature.
Bio::Tools::Primer3(3pm)	Create input for and work with the output from the program primer3.
Bio::Tools::Primer::Assessor::Base(3pm)	Base class for common assessor things.
Bio::Tools::Primer::AssessorI(3pm)	Interface for assessing primer pairs.
Bio::Tools::Primer::Feature(3pm)	Position of a single primer.
Bio::Tools::Primer::Pair(3pm)	Two primers on left and right side.
Bio::Tools::Prints(3pm)	Parser for FingerPRINTScanII program.
Bio::Tools::Profile(3pm)	Parse Profile output.
Bio::Tools::Promoterwise(3pm)	Parser for Promoterwise tab format output.
Bio::Tools::PrositeScan(3pm)	Parser for ps_scan result.
Bio::Tools::Protparam(3pm)	Submit to and parse output from protparam ;.
Bio::Tools::Pseudowise(3pm)	Results of one Pseudowise run.
Bio::Tools::pSW(3pm)	Pairwise Smith Waterman object.
Bio::Tools::QRNA(3pm)	A Parser for qrna output.
Bio::Tools::RandomDistFunctions(3pm)	A set of routines useful for generating random data in different.
Bio::Tools::RepeatMasker(3pm)	A parser for RepeatMasker output.
Bio::Tools::RNAMotif(3pm)	A parser for RNAMotif output.
Bio::Tools::Run::Alignment::Amap(3pm)	Object for the calculation of an iterative multiple sequence alignment from.
Bio::Tools::Run::Alignment::Blat(3pm)	…
Bio::Tools::Run::Alignment::Clustalw(3pm)	Object for the calculation of a multiple sequence alignment from a set.
Bio::Tools::Run::Alignment::DBA(3pm)	Object for the alignment of two sequences using the DNA Block Aligner.
Bio::Tools::Run::Alignment::Exonerate(3pm)	…
Bio::Tools::Run::Alignment::Gmap(3pm)	Wrapper for running gmap.
Bio::Tools::Run::Alignment::Kalign(3pm)	Object for the calculation of an iterative multiple sequence alignment.
Bio::Tools::Run::Alignment::Lagan(3pm)	Object for the local execution of the LAGAN suite of tools (including.
Bio::Tools::Run::Alignment::MAFFT(3pm)	Run the MAFFT alignment tools.
Bio::Tools::Run::Alignment::Muscle(3pm)	Object for the calculation of an iterative multiple sequence alignment.
Bio::Tools::Run::Alignment::Pal2Nal(3pm)	Wrapper for Pal2Nal.
Bio::Tools::Run::Alignment::Probalign(3pm)	Object for the calculation of a multiple sequence alignment from a set.
Bio::Tools::Run::Alignment::Probcons(3pm)	Object for the calculation of an iterative multiple sequence alignment.
Bio::Tools::Run::Alignment::Proda(3pm)	Object for the calculation of sets of multiple sequence alignments from a.
Bio::Tools::Run::Alignment::Sim4(3pm)	Wrapper for Sim4 program that allows for alignment of cdna to genomic.
Bio::Tools::Run::Alignment::StandAloneFasta(3pm)	Object for the local execution of the Fasta3 programs.
Bio::Tools::Run::Alignment::TCoffee(3pm)	Object for the calculation of a multiple sequence alignment from a set.
Bio::Tools::Run::Analysis(3pm)	Module representing any (remote or local) analysis tool.
Bio::Tools::Run::Analysis::soap(3pm)	A SOAP-based access to the analysis tools.
Bio::Tools::Run::AnalysisFactory(3pm)	A directory of analysis tools.
Bio::Tools::Run::AnalysisFactory::soap(3pm)	A SOAP-based access to the list of analysis tools.
Bio::Tools::Run::AssemblerBase(3pm)	Base class for wrapping external assemblers.
Bio::Tools::Run::BEDTools(3pm)	Run wrapper for the BEDTools suite of programs BETA.
Bio::Tools::Run::BEDTools::Config(3pm)	Configuration data for bowtie commands.
Bio::Tools::Run::BlastPlus(3pm)	A wrapper for NCBI's blast+ suite.
Bio::Tools::Run::Bowtie(3pm)	Run wrapper for the Bowtie short-read assembler BETA.
Bio::Tools::Run::Bowtie::Config(3pm)	Configuration data for bowtie commands.
Bio::Tools::Run::BWA(3pm)	Run wrapper for the BWA short-read assembler BETA.
Bio::Tools::Run::BWA::Config(3pm)	Configuration data for BWA commands.
Bio::Tools::Run::Cap3(3pm)	Wrapper for CAP3.
Bio::Tools::Run::Coil(3pm)	Wrapper for ncoils program.
Bio::Tools::Run::EMBOSSacd(3pm)	Class for EMBOSS Application qualifiers.
Bio::Tools::Run::EMBOSSApplication(3pm)	Class for EMBOSS Applications.
Bio::Tools::Run::Ensembl(3pm)	A simplified front-end for setting up the registry.
Bio::Tools::Run::Eponine(3pm)	Object for execution of the Eponine which is a mammalian TSS predictor.
Bio::Tools::Run::ERPIN(3pm)	Wrapper for local execution of the ERPIN suite of programs.
Bio::Tools::Run::FootPrinter(3pm)	Wrapper for the FootPrinter program.
Bio::Tools::Run::Genemark(3pm)	Wrapper for local execution of the GeneMark family of programs.
Bio::Tools::Run::GenericParameters(3pm)	An object for the parameters used to run programs.
Bio::Tools::Run::Genewise(3pm)	Object for predicting genes in a given sequence given a protein.
Bio::Tools::Run::Genscan(3pm)	Object for identifying genes in a given sequence given a matrix(for appropriate.
Bio::Tools::Run::Glimmer(3pm)	Wrapper for local execution of Glimmer, GlimmerM and GlimmerHMM.
Bio::Tools::Run::Hmmer(3pm)	Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam,.
Bio::Tools::Run::Infernal(3pm)	Wrapper for local execution of cmalign, cmbuild, cmsearch, cmscore.
Bio::Tools::Run::Maq(3pm)	Run wrapper for the Maq short-read assembler BETA.
Bio::Tools::Run::Maq::Config(3pm)	Configuration data for maq commands.
Bio::Tools::Run::Match(3pm)	Wrapper for Transfac's match(TM).
Bio::Tools::Run::MCS(3pm)	Wrapper for MCS.
Bio::Tools::Run::Mdust(3pm)	Perl extension for Mdust nucleotide filtering.
Bio::Tools::Run::Meme(3pm)	Wrapper for Meme Program.
Bio::Tools::Run::Minimo(3pm)	Wrapper for local execution of the Minimo assembler.
Bio::Tools::Run::Newbler(3pm)	Wrapper for local execution of Newbler.
Bio::Tools::Run::ParametersI(3pm)	A Base object for the parameters used to run programs.
Bio::Tools::Run::Phrap(3pm)	A wrapper for running Phrap.
Bio::Tools::Run::Phylo::Gerp(3pm)	Wrapper for GERP.
Bio::Tools::Run::Phylo::Gumby(3pm)	Wrapper for gumby.
Bio::Tools::Run::Phylo::Hyphy::Base(3pm)	Hyphy wrapping base methods.
Bio::Tools::Run::Phylo::Hyphy::FEL(3pm)	Wrapper around the Hyphy FEL analysis.
Bio::Tools::Run::Phylo::Hyphy::Modeltest(3pm)	Wrapper around the Hyphy Modeltest analysis.
Bio::Tools::Run::Phylo::Hyphy::REL(3pm)	Wrapper around the Hyphy REL analysis.
Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm)	Wrapper around the Hyphy SLAC analysis.
Bio::Tools::Run::Phylo::LVB(3pm)	Object for using the LVB program to create an array of Bio::Tree objects from a.
Bio::Tools::Run::Phylo::Molphy::ProtML(3pm)	A wrapper for the Molphy pkg app ProtML.
Bio::Tools::Run::Phylo::Njtree::Best(3pm)	Wrapper around the Njtree (Njtree/phyml) best program.
Bio::Tools::Run::Phylo::PAML::Baseml(3pm)	Wrapper aroud the PAML program baseml.
Bio::Tools::Run::Phylo::PAML::Codeml(3pm)	Wrapper aroud the PAML program codeml.
Bio::Tools::Run::Phylo::PAML::Evolver(3pm)	Wrapper aroud the PAML program evolver.
Bio::Tools::Run::Phylo::PAML::Yn00(3pm)	Wrapper aroud the PAML program yn00.
Bio::Tools::Run::Phylo::Phast::PhastCons(3pm)	Wrapper for footprinting using.
Bio::Tools::Run::Phylo::Phast::PhyloFit(3pm)	Wrapper for phyloFit.
Bio::Tools::Run::Phylo::Phylip::Base(3pm)	Base object for Phylip modules.
Bio::Tools::Run::Phylo::Phylip::Consense(3pm)	Wrapper for the phylip program Consense.
Bio::Tools::Run::Phylo::Phylip::DrawGram(3pm)	Use Phylip DrawTree program to draw phylograms or phenograms.
Bio::Tools::Run::Phylo::Phylip::DrawTree(3pm)	Use Phylip DrawTree program to draw trees.
Bio::Tools::Run::Phylo::Phylip::Neighbor(3pm)	Wrapper for the phylip program neighbor by Joseph Felsenstein for.
Bio::Tools::Run::Phylo::Phylip::PhylipConf(3pm)	…
Bio::Tools::Run::Phylo::Phylip::ProtDist(3pm)	Wrapper for the phylip program protdist.
Bio::Tools::Run::Phylo::Phylip::ProtPars(3pm)	Object for creating a Bio::Tree object from a multiple alignment.
Bio::Tools::Run::Phylo::Phylip::SeqBoot(3pm)	Wrapper for the phylip program SeqBoot.
Bio::Tools::Run::Phylo::PhyloBase(3pm)	…
Bio::Tools::Run::Phylo::Phyml(3pm)	Wrapper for rapid reconstruction of phylogenies using Phyml.
Bio::Tools::Run::Phylo::QuickTree(3pm)	Wrapper for rapid reconstruction of.
Bio::Tools::Run::Phylo::Semphy(3pm)	Wrapper for Semphy.
Bio::Tools::Run::Phylo::SLR(3pm)	Wrapper around the SLR program.
Bio::Tools::Run::Primate(3pm)	…
Bio::Tools::Run::Primer3(3pm)	Create input for and work with the output from the program primer3.
Bio::Tools::Run::Prints(3pm)	…
Bio::Tools::Run::Profile(3pm)	…
Bio::Tools::Run::Promoterwise(3pm)	Wrapper for aligning two sequences using promoterwise.
Bio::Tools::Run::Pseudowise(3pm)	Object for prediting pseudogenes in a given sequence given a protein and a cdna.
Bio::Tools::Run::RemoteBlast(3pm)	Object for remote execution of the NCBI Blast via HTTP.
Bio::Tools::Run::RepeatMasker(3pm)	Wrapper for RepeatMasker Program.
Bio::Tools::Run::RNAMotif(3pm)	Wrapper for local execution of rnamotif, rm2ct, rmfmt, rmprune.
Bio::Tools::Run::Samtools(3pm)	A run wrapper for the samtools suite BETA.
Bio::Tools::Run::Samtools::Config(3pm)	Configurator for Bio::Tools::Run::Samtools.
Bio::Tools::Run::Seg(3pm)	Object for identifying low complexity.
Bio::Tools::Run::Signalp(3pm)	…
Bio::Tools::Run::Simprot(3pm)	Wrapper around the Simprot program. Wrapper for the calculation of a multiple.
Bio::Tools::Run::StandAloneBlast(3pm)	Object for the local execution of the NCBI BLAST program suite (blastall,.
Bio::Tools::Run::StandAloneBlastPlus(3pm)	Compute with NCBI's blast+ suite ALPHA.
Bio::Tools::Run::StandAloneBlastPlus::BlastMethods(3pm)	Provides BLAST methods to StandAloneBlastPlus.
Bio::Tools::Run::StandAloneNCBIBlast(3pm)	Object for the local execution of the NCBI BLAST program suite.
Bio::Tools::Run::StandAloneWUBlast(3pm)	Object for the local execution of WU-Blast.
Bio::Tools::Run::TigrAssembler(3pm)	Wrapper for local execution of TIGR Assembler.
Bio::Tools::Run::Tmhmm(3pm)	Object for identifying transmembrane helixes.
Bio::Tools::Run::TribeMCL(3pm)	…
Bio::Tools::Run::tRNAscanSE(3pm)	Wrapper for local execution of tRNAscan-SE.
Bio::Tools::Run::Vista(3pm)	…
Bio::Tools::Run::WrapperBase(3pm)	A Base object for wrappers around executables.
Bio::Tools::Run::WrapperBase::CommandExts(3pm)	Extensions to WrapperBase for handling programs with commands.
Bio::Tools::Seg(3pm)	Parse "seg" output.
Bio::Tools::SeqPattern(3pm)	Represent a sequence pattern or motif.
Bio::Tools::SeqPattern::Backtranslate(3pm)	…
Bio::Tools::SeqStats(3pm)	Object holding statistics for one particular sequence.
Bio::Tools::SeqWords(3pm)	Object holding n-mer statistics for a sequence.
Bio::Tools::Sigcleave(3pm)	Bioperl object for sigcleave analysis.
Bio::Tools::Signalp(3pm)	Parser for Signalp output.
Bio::Tools::Signalp::ExtendedSignalp(3pm)	Enhanced parser for Signalp output.
Bio::Tools::Sim4::Exon(3pm)	A single exon determined by an alignment.
Bio::Tools::Sim4::Results(3pm)	Results of one Sim4 run.
Bio::Tools::SiRNA(3pm)	Perl object for designing small inhibitory RNAs.
Bio::Tools::SiRNA::Ruleset::saigo(3pm)	Perl object implementing the Saigo group's rules for designing small.
Bio::Tools::SiRNA::Ruleset::tuschl(3pm)	Perl object implementing the tuschl group's rules for designing small.
Bio::Tools::Spidey::Exon(3pm)	A single exon determined by an alignment.
Bio::Tools::Spidey::Results(3pm)	Results of a Spidey run.
Bio::Tools::TandemRepeatsFinder(3pm)	A parser for Tandem Repeats Finder output.
Bio::Tools::TargetP(3pm)	Results of one TargetP run.
Bio::Tools::Tmhmm(3pm)	Parse TMHMM output (TransMembrane HMM).
Bio::Tools::tRNAscanSE(3pm)	A parser for tRNAscan-SE output.
Bio::Tree::AlleleNode(3pm)	A Node with Alleles attached.
Bio::Tree::AnnotatableNode(3pm)	A Tree Node with support for annotation.
Bio::Tree::Compatible(3pm)	Testing compatibility of phylogenetic trees with nested taxa.
Bio::Tree::DistanceFactory(3pm)	Construct a tree using distance based methods.
Bio::Tree::Draw::Cladogram(3pm)	Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
Bio::Tree::Node(3pm)	A Simple Tree Node.
Bio::Tree::NodeI(3pm)	Interface describing a Tree Node.
Bio::Tree::NodeNHX(3pm)	A Simple Tree Node with support for NHX tags.
Bio::Tree::RandomFactory(3pm)	TreeFactory for generating Random Trees.
Bio::Tree::Statistics(3pm)	Calculate certain statistics for a Tree.
Bio::Tree::Tree(3pm)	An implementation of the TreeI interface.
Bio::Tree::TreeFunctionsI(3pm)	Decorated Interface implementing basic Tree exploration methods.
Bio::Tree::TreeI(3pm)	A Tree object suitable for lots of things, designed.
Bio::TreeIO(3pm)	Parser for Tree files.
Bio::TreeIO::cluster(3pm)	A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output.
Bio::TreeIO::lintree(3pm)	Parser for lintree output trees.
Bio::TreeIO::newick(3pm)	…
Bio::TreeIO::NewickParser(3pm)	…
Bio::TreeIO::nexml(3pm)	A TreeIO driver module for parsing NeXML tree files.
Bio::TreeIO::nexus(3pm)	A TreeIO driver module for parsing Nexus tree output from PAUP.
Bio::TreeIO::nhx(3pm)	TreeIO implementation for parsing.
Bio::TreeIO::pag(3pm)	Bio::TreeIO driver for Pagel format.
Bio::TreeIO::phyloxml(3pm)	TreeIO implementation for parsing PhyloXML format.
Bio::TreeIO::svggraph(3pm)	A simple output format that converts a Tree object to an SVG output.
Bio::TreeIO::tabtree(3pm)	A simple output format which displays a tree as an ASCII drawing.
Bio::TreeIO::TreeEventBuilder(3pm)	Build Bio::Tree::Tree's and.
Bio::UpdateableSeqI(3pm)	Descendant of Bio::SeqI that allows updates.
Bio::Variation::AAChange(3pm)	Sequence change class for polypeptides.
Bio::Variation::AAReverseMutate(3pm)	Point mutation and codon.
Bio::Variation::Allele(3pm)	Sequence object with allele-specific attributes.
Bio::Variation::DNAMutation(3pm)	DNA level mutation class.
Bio::Variation::IO(3pm)	Handler for sequence variation IO Formats.
Bio::Variation::IO::flat(3pm)	Flat file sequence variation input/output stream.
Bio::Variation::IO::xml(3pm)	XML sequence variation input/output stream.
Bio::Variation::RNAChange(3pm)	Sequence change class for RNA level.
Bio::Variation::SeqDiff(3pm)	Container class for mutation/variant descriptions.
Bio::Variation::SNP(3pm)	Submitted SNP.
Bio::Variation::VariantI(3pm)	Sequence Change SeqFeature abstract class.
Bio::WebAgent(3pm)	A base class for Web (any protocol) access.
bisque(3pm) ↣ Tk::palette(3pm)	Modify the Tk color palette.
Bit::Vector(3pm)	Efficient bit vector, set of integers and "big int" math library.
Bit::Vector::Minimal(3pm)	Object-oriented wrapper around vec().
Bit::Vector::Overload(3pm)	Overloaded operators add-on for Bit::Vector.
Bit::Vector::String(3pm)	Generic string import/export for Bit::Vector.
blhc(1)	Build log hardening check, checks build logs for missing hardening flags.
blinkenlights(1p)	DNSSEC-Tools rollerd GUI.
blinkenlights.conf(5)	Configuration file for the DNSSEC-Tools B.
Bloom::Filter(3pm)	Sample Perl Bloom filter implementation.
bones-info(1)	Display information about a Nethack bones file.
boolean(3pm)	Boolean support for Perl.
Boost::Geometry::Utils(3pm)	Bindings for the Boost Geometry library.
bot-basicbot-pluggable(1p)	A standard Bot::BasicBot::Pluggable script.
bot-basicbot-pluggable-cgi(1p)	A standard Bot::BasicBot::Pluggable script.
bot-training(1p)	Command-line interface Bot::Training.
Bot::BasicBot(3pm)	Simple irc bot baseclass.
Bot::BasicBot::Pluggable(3pm)	Extended simple IRC bot for pluggable modules.
Bot::BasicBot::Pluggable::Module(3pm)	Base module for all BasicBot plugins.
Bot::BasicBot::Pluggable::Module::Auth(3pm)	Authentication for Bot::BasicBot::Pluggable modules.
Bot::BasicBot::Pluggable::Module::ChanOp(3pm)	Channel operator.
Bot::BasicBot::Pluggable::Module::DNS(3pm)	DNS lookups for hostnames or IP addresses.
Bot::BasicBot::Pluggable::Module::Google(3pm)	Searches Google for terms and spellings.
Bot::BasicBot::Pluggable::Module::Infobot(3pm)	Infobot clone redone in B::B::P.
Bot::BasicBot::Pluggable::Module::Join(3pm)	Join and leave channels; remembers state.
Bot::BasicBot::Pluggable::Module::Karma(3pm)	Tracks karma for various concepts.
Bot::BasicBot::Pluggable::Module::Loader(3pm)	Loads and unloads bot modules; remembers state.
Bot::BasicBot::Pluggable::Module::Seen(3pm)	Track when and where people were seen.
Bot::BasicBot::Pluggable::Module::Title(3pm)	Speaks the title of URLs mentioned.
Bot::BasicBot::Pluggable::Module::Vars(3pm)	Change internal module variables.
Bot::BasicBot::Pluggable::Store(3pm)	Base class for the back-end pluggable store.
Bot::BasicBot::Pluggable::Store::DBI(3pm)	Use DBI to provide a storage backend.
Bot::BasicBot::Pluggable::Store::Deep(3pm)	Use DBM::Deep to provide a storage backend.
Bot::BasicBot::Pluggable::Store::Memory(3pm)	Use memory (RAM) to provide a storage backend.
Bot::BasicBot::Pluggable::Store::Storable(3pm)	Use Storable to provide a storage backend.
Bot::BasicBot::Pluggable::Terminal(3pm)	A standard Bot::BasicBot::Pluggable script.
Bot::Training(3pm)	Plain text training material for bots like Hailo and AI::MegaHAL.
Boulder(3pm)	An API for hierarchical tag/value structures.
Boulder::Blast(3pm)	Parse and read BLAST files.
Boulder::Blast::NCBI(3pm)	Parse and read NCBI BLAST files.
Boulder::Blast::WU(3pm)	Parse and read WU-BLAST files.
Boulder::Genbank(3pm)	Fetch Genbank data records as parsed Boulder Stones.
Boulder::LocusLink(3pm)	Fetch LocusLink data records as parsed Boulder Stones.
Boulder::Medline(3pm)	Fetch Medline data records as parsed Boulder Stones.
Boulder::Omim(3pm)	Fetch Omim data records as parsed Boulder Stones.
Boulder::Store(3pm)	Simple persistent storage for Stone tag/value objects.
Boulder::Stream(3pm)	Read and write tag/value data from an input stream.
Boulder::String(3pm)	Read and write tag/value data from a string.
Boulder::Swissprot(3pm)	Fetch SwissProt data records as parsed Boulder Stones.
Boulder::Unigene(3pm)	Fetch Unigene data records as parsed Boulder Stones.
Boulder::XML(3pm)	XML format input/output for Boulder streams.
boxer(1p)	Boxer command line utils.
Boxer(3pm)	System deployment ninja tricks.
Boxer::CLI(3pm)	Boxer command line utils.
bp_aacomp(1p)	Amino acid composition of protein sequences.
bp_biofetch_genbank_proxy(1p)	Caching BioFetch-compatible web proxy for GenBank.
bp_bioflat_index(1p)	Index sequence files using Bio::DB::Flat.
bp_biogetseq(1p)	Sequence retrieval using OBDA registry.
bp_bioperl_application_installer.pl(1p)	Downloads and installs runnables.
bp_blast2tree(1p)	Builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER).
bp_bulk_load_gff(1p)	Bulk-load a Bio::DB::GFF database from GFF files.
bp_chaos_plot(1p)	A chaos plot from DNA and RNA sequences.
bp_classify_hits_kingdom(1p)	Classify BLAST hits by taxonomic kingdom.
bp_composite_LD(1p)	…
bp_dbsplit(1p)	Script to split an input set of database(s) into smaller pieces.
bp_download_query_genbank(1p)	Script to query Genbank and retrieve records.
bp_extract_feature_seq(1p)	Extract the corresponding sequence for a specified feature type.
bp_fast_load_gff(1p)	Fast-load a Bio::DB::GFF database from GFF files.
bp_fastam9_to_table(1p)	Turn FASTA -m 9 output into NCBI -m 9 tabular output.
bp_fetch(1p)	Fetches sequences from bioperl indexed databases.
bp_filter_search(1p)	Filters searchio results, outputting a tab delimited summary.
bp_flanks(1p)	Finding flanking sequences for a variant in a sequence position.
bp_gccalc(1p)	GC content of nucleotide sequences.
bp_genbank2gff(1p)	Load a Bio::DB::GFF database from GENBANK files.
bp_genbank2gff3(1p)	…
bp_generate_histogram(1p)	…
bp_heterogeneity_test(1p)	A test for distinguishing between selection and population expansion.
bp_hivq(1p)	An interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery.
bp_hmmer_to_table(1p)	Turn HMMER output into tabular format.
bp_index(1p)	Indexes files for use by bp_fetch.pl.
bp_load_gff(1p)	Load a Bio::DB::GFF database from GFF files.
bp_local_taxonomydb_query(1p)	Query a local TaxonomyDB for species or taxonid.
bp_make_mrna_protein(1p)	Convert an input mRNA/cDNA sequence into protein.
bp_mask_by_search(1p)	Mask sequence(s) based on its alignment results.
bp_meta_gff(1p)	Get/set Bio::DB::GFF meta-data.
bp_mrtrans(1p)	Implement a transformer of alignments from protein to mrna coordinates.
bp_multi_hmmsearch.pl(1p)	Perform a hmmsearch into multiple FASTA files using.
bp_mutate(1p)	Randomly mutagenize a single protein or DNA sequence.
bp_netinstall(1p)	…
bp_nexus2nh(1p)	Convert nexus format trees (from PAUP* and MrBayes) to new hampshire.
bp_nrdb(1p)	A script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input.
bp_oligo_count(1p)	Oligo count and frequency.
bp_pairwise_kaks(1p)	Script to calculate pairwise Ka,Ks for a set of sequences.
bp_panalysis.pl(1p)	An example/tutorial script how to access analysis tools.
bp_papplmaker.pl(1p)	Analysis tools module generator.
bp_parse_hmmsearch(1p)	Parse single/multiple HMMSEARCH results file(s) with.
bp_process_gadfly(1p)	Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser.
bp_process_sgd(1p)	Massage SGD annotation flat files into a version suitable for the Generic Genome Browser.
bp_process_wormbase(1p)	Massage WormBase GFF files into a version suitable for the Generic Genome Browser.
bp_query_entrez_taxa(1p)	Query Entrez taxonomy database and print out information.
bp_remote_blast(1p)	Script for submitting jobs to a remote blast server (ncbi blast queue at this time).
bp_revtrans-motif(1p)	Reverse translate a Profam-like protein motif.
bp_run_neighbor.pl(1p)	Run Phylip's 'neighbor' program through Bioperl.
bp_run_protdist.pl(1p)	Run Phylip's 'protdist' program through Bioperl.
bp_search2alnblocks(1p)	Turn SearchIO parseable reports(s) into a set of aligned blocks.
bp_search2BSML(1p)	Turn SearchIO parseable reports(s) into a BSML report.
bp_search2gff(1p)	…
bp_search2table(1p)	Turn SearchIO parseable reports into tab delimited format like NCBI's -m 9.
bp_search2tribe(1p)	Turn SearchIO parseable reports(s) into TRIBE matrix.
bp_seq_length(1p)	Lists the number of bases and number of sequences in specified sequence database files.
bp_seqconvert(1p)	Generic BioPerl sequence format converter.
bp_seqcut(1p)	…
bp_seqfeature_load(1p)	Load GFF into a SeqFeature database.
bp_seqpart(1p)	Takes one or more sequence files and splits them into a number of load balanced files.
bp_seqret(1p)	Bioperl implementation of sequence fetch from local db (like EMBOSS seqret).
bp_seqretsplit(1p)	Split a sequence (or stream) into a single file per sequence.
bp_split_seq(1p)	Splits a sequence into equal sized chunks with an optional.
bp_sreformat(1p)	Convert sequence formats.
bp_taxid4species(1p)	Simple script which returns the NCBI Taxonomic id for a requested species.
bp_taxonomy2tree(1p)	Building a taxonomic tree based on the full lineages of a set of species names.
bp_translate_seq(1p)	Translates a sequence.
bp_tree2pag(1p)	Convert Bio::TreeIO parseable format trees to pagel format.
bp_unflatten_seq(1p)	Unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy.
Bread::Board(3pm)	A solderless way to wire up your application components.
Bread::Board::BlockInjection(3pm)	…
Bread::Board::ConstructorInjection(3pm)	…
Bread::Board::Container(3pm)	…
Bread::Board::Container::FromParameterized(3pm)	…
Bread::Board::Container::Parameterized(3pm)	A parameterized container.
Bread::Board::Dependency(3pm)	…
Bread::Board::Dumper(3pm)	…
Bread::Board::LifeCycle(3pm)	…
Bread::Board::LifeCycle::Singleton(3pm)	…
Bread::Board::LifeCycle::Singleton::WithParameters(3pm)	…
Bread::Board::Literal(3pm)	…
Bread::Board::Manual(3pm)	A manual for Bread::Board.
Bread::Board::Manual::Concepts(3pm)	An overview of the concepts in Bread::Board.
Bread::Board::Manual::Concepts::Advanced(3pm)	An overview of some of the more advanced Bread::Board concepts.
Bread::Board::Manual::Concepts::Typemap(3pm)	An overview of the typemapping feature.
Bread::Board::Manual::Example(3pm)	A set of examples of Bread::Board usage.
Bread::Board::Manual::Example::FormSensible(3pm)	A Form::Sensible and Catalyst example.
Bread::Board::Manual::Example::LogDispatch(3pm)	An example of composing a dynamic Log::Dispatch object.
Bread::Board::Service(3pm)	…
Bread::Board::Service::Alias(3pm)	…
Bread::Board::Service::Deferred(3pm)	…
Bread::Board::Service::Deferred::Thunk(3pm)	…
Bread::Board::Service::Inferred(3pm)	…
Bread::Board::Service::WithClass(3pm)	…
Bread::Board::Service::WithDependencies(3pm)	…
Bread::Board::Service::WithParameters(3pm)	…
Bread::Board::SetterInjection(3pm)	…
Bread::Board::Traversable(3pm)	…
Bread::Board::Types(3pm)	…
Browser::Open(3pm)	Open a browser in a given URL.
BSD::arc4random(3pm)	Perl interface to the arc4 random number generator.
BSD::Resource(3pm)	BSD process resource limit and priority functions.
bubbles(1p)	DNSSEC-Tools Rollrec Simple GUI Display.
bucardo(1p)	Utility script for controlling the Bucardo program.
Bucardo(3pm)	Postgres multi-master replication system.
buffycli(1p)	Text mode alternative to Buffy. Monitors new and unread messages in a collection of mail folders.
buildrealms(1p)	Assist in building a DNSSEC-Tools realms environment.
Bundle::Apache2(3pm)	Install Apache mod_perl2 and related modules.
Bundle::Apache::ASP(3pm)	Install Apache::ASP and required.
Bundle::Apache::ASP::Extra(3pm)	Install modules that provide additional functionality to Apache::ASP.
Bundle::ApacheTest(3pm)	A bundle to install all Apache-Test related modules.
Bundle::DBD::CSV(3pm)	A bundle to install the DBD::CSV driver.
Bundle::DBD::Pg(3pm)	A bundle to install all DBD::Pg related modules.
Bundle::DBI(3pm)	A bundle to install DBI and required modules.
Bundle::Net::LDAP(3pm)	A bundle for Net::LDAP.
Bundle::Object::InsideOut(3pm)	A bundle of modules for full Object::InsideOut support.
Bundle::pRPC-modules(3pm)	A bundle to install pRPC-modules and prerequisites.
Bundle::SNMP::MIB::Compiler(3pm)	A bundle to install all SNMP::MIB::Compiler related modules.
Business-ISSN(3pm)	Perl extension for International Standard Serial Numbers.
Business::BR(3pm)	Root for namespace of Brazilian business-related modules.
Business::BR::Biz(3pm)	DEPRECATED (was: Modules for Brazilian business-related subjects).
Business::BR::CNPJ(3pm)	Perl module to test for correct CNPJ numbers.
Business::BR::CPF(3pm)	Perl module to test for correct CPF numbers.
Business::BR::Ids(3pm)	Modules for dealing with Brazilian identification codes (CPF, CNPJ, ...).
Business::BR::Ids::Common(3pm)	Common code used in Business-BR-Ids modules.
Business::BR::IE(3pm)	Perl module to test for correct IE numbers.
Business::BR::PIS(3pm)	Perl module to test for correct PIS numbers.
Business::CreditCard(3pm)	Validate/generate credit card checksums/names.
Business::EDI(3pm)	Top level class for generating U.N. EDI interchange objects and subobjects.
Business::EDI::CodeList(3pm)	Abstract object class for UN/EDIFACT objects that do not have further descendant.
Business::EDI::Composite(3pm)	EDI Composite class.
Business::EDI::Spec(3pm)	Object class for CSV-based U.N. EDI specifications.
Business::Edifact::Interchange(3pm)	Parse Edifact Messages For Book Ordering.
Business::Edifact::Message(3pm)	Class that models Edifact Messages.
Business::Edifact::Message::LineItem(3pm)	Model an individual Item Line in a message.
Business::FraudDetect(3pm)	A cohort to Business::OnlinePayment.
Business::FraudDetect::preCharge(3pm)	Backend for Business::FraudDetect (part of Business::OnlinePayment).
Business::ISBN(3pm)	Work with International Standard Book Numbers.
Business::ISBN10(3pm)	Work with 10 digit International Standard Book Numbers.
Business::ISBN13(3pm)	Work with 13 digit International Standard Book Numbers.
Business::ISBN::Data(3pm)	Data pack for Business::ISBN.
Business::ISMN(3pm)	Work with International Standard Music Numbers.
Business::ISMN::Data(3pm)	Data pack for Business::ISMN.
Business::OnlinePayment(3pm)	Perl extension for online payment processing.
Business::OnlinePayment::AuthorizeNet(3pm)	AuthorizeNet backend for Business::OnlinePayment.
Business::OnlinePayment::AuthorizeNet::AIM(3pm)	AuthorizeNet AIM backend for Business::OnlinePayment.
Business::OnlinePayment::AuthorizeNet::AIM::ErrorCodes(3pm)	Easy lookup of Authorize.Net's AIM result reason.
Business::OnlinePayment::AuthorizeNet::ARB(3pm)	AuthorizeNet ARB backend for Business::OnlinePayment.
Business::OnlinePayment::HTTPS(3pm)	Base class for HTTPS payment APIs.
Business::OnlinePayment::IPPay(3pm)	IPPay backend for Business::OnlinePayment.
Business::OnlinePayment::OpenECHO(3pm)	ECHO backend module for Business::OnlinePayment.
Business::OnlinePayment::PayConnect(3pm)	PaymentOne (formerly eBillit) PayConnect backend for.
Business::OnlinePayment::PayflowPro(3pm)	Payflow Pro backend for Business::OnlinePayment.
Business::OnlinePayment::PaymenTech(3pm)	Chase Paymentech backend for Business::OnlinePayment.
Business::OnlinePayment::TCLink(3pm)	TrustCommerce backend for Business::OnlinePayment.
Business::OnlinePayment::TransactionCentral(3pm)	Transaction Central backend module for Business::OnlinePayment.
Business::OnlinePayment::viaKLIX(3pm)	ViaKLIX backend for Business::OnlinePayment.
Business::PayPal::API(3pm)	PayPal SOAP API client with sandbox support.
Business::PayPal::API::AuthorizationRequest(3pm)	PayPal AuthorizationRequest API.
Business::PayPal::API::CaptureRequest(3pm)	PayPal CaptureRequest API.
Business::PayPal::API::DirectPayments(3pm)	PayPal DirectPayments API.
Business::PayPal::API::ExpressCheckout(3pm)	PayPal Express Checkout API.
Business::PayPal::API::GetBalance(3pm)	PayPal GetBalance API.
Business::PayPal::API::GetTransactionDetails(3pm)	PayPal GetTransactionDetails API.
Business::PayPal::API::MassPay(3pm)	PayPal MassPay API.
Business::PayPal::API::ReauthorizationRequest(3pm)	PayPal ReauthorizationRequest API.
Business::PayPal::API::RecurringPayments(3pm)	PayPal RecurringPayments API.
Business::PayPal::API::RefundTransaction(3pm)	PayPal RefundTransaction API.
Business::PayPal::API::TransactionSearch(3pm)	PayPal TransactionSearch API.
Business::PayPal::API::VoidRequest(3pm)	PayPal VoidRequest API.
Business::Tax::VAT::Validation(3pm)	Validate EU VAT numbers against VIES.
Business::US::USPS::WebTools(3pm)	Use the US Postal Service Web Tools.
Bytes::Random::Secure(3pm)	Perl extension to generate cryptographically-secure random bytes.
Cache(3pm)	The Cache interface.
Cache.pm(3)	Octopussy Cache module.
Cache::BaseCache(3pm)	…
Cache::BaseCacheTester(3pm)	…
Cache::BDB(3pm)	An object caching wrapper around BerkeleyDB.
Cache::Cache(3pm)	…
Cache::CacheMetaData(3pm)	…
Cache::CacheSizer(3pm)	…
Cache::CacheTester(3pm)	…
Cache::CacheUtils(3pm)	…
Cache::Entry(3pm)	Interface for a cache entry.
Cache::FastMmap(3pm)	Uses an mmap'ed file to act as a shared memory interprocess cache.
Cache::File(3pm)	Filesystem based implementation of the Cache interface.
Cache::File::Entry(3pm)	An entry in the file based implementation of Cache.
Cache::File::Handle(3pm)	Wrapper for IO::File to use in Cache::File implementation.
Cache::File::Heap(3pm)	A file based heap for use by Cache::File.
Cache::FileBackend(3pm)	…
Cache::FileCache(3pm)	…
Cache::Historical(3pm)	Cache historical values.
Cache::IOString(3pm)	Wrapper for IO::String to use in Cache implementations.
Cache::LRU(3pm)	A simple, fast implementation of LRU cache in pure perl.
Cache::Memcached(3pm)	Client library for memcached (memory cache daemon).
Cache::Memcached::Fast(3pm)	Perl client for memcached, in C language.
Cache::Memcached::GetParserXS(3pm)	GetParser implementation in XS for use with Cache::Memcached.
Cache::Memcached::Managed(3pm)	Provide API for managing cached information.
Cache::Memcached::Managed::Inactive(3pm)	Inactive Cache::Memcache::Managed object.
Cache::Memcached::Managed::Multi(3pm)	Multiple Cache::Memcache::Managed objects.
Cache::Memory(3pm)	Memory based implementation of the Cache interface.
Cache::Memory::Entry(3pm)	An entry in the memory based implementation of Cache.
Cache::Memory::HeapElem(3pm)	Wrapper for Heap::Elem that stores keys.
Cache::MemoryBackend(3pm)	…
Cache::MemoryCache(3pm)	…
Cache::Mmap(3pm)	Shared data cache using memory mapped files.
Cache::Null(3pm)	Null implementation of the Cache interface.
Cache::Null::Entry(3pm)	An entry in the Null implementation of Cache.
Cache::NullCache(3pm)	…
Cache::Object(3pm)	…
Cache::Ref(3pm)	Memory only cache of live references.
Cache::Ref::CAR(3pm)	CLOCK with Adaptive Replacement.
Cache::Ref::CAR::Base(3pm)	Base clase for CAR and CART.
Cache::Ref::CART(3pm)	CAR with temporal filtering.
Cache::Ref::CLOCK(3pm)	CLOCK cache replacement algorithm.
Cache::Ref::CLOCK::Base(3pm)	…
Cache::Ref::FIFO(3pm)	…
Cache::Ref::GCLOCK(3pm)	GCLOCK cache replacement algorithm.
Cache::Ref::LIFO(3pm)	Saves entries until full, discarding subsequent sets.
Cache::Ref::LRU(3pm)	Least recently used expiry policy.
Cache::Ref::Null(3pm)	Caches nothing.
Cache::Ref::Random(3pm)	…
Cache::Ref::Role::API(3pm)	…
Cache::Ref::Role::Index(3pm)	…
Cache::Ref::Role::WithDoublyLinkedList(3pm)	…
Cache::Ref::Util::LRU::API(3pm)	…
Cache::Ref::Util::LRU::Array(3pm)	…
Cache::Ref::Util::LRU::List(3pm)	…
Cache::RemovalStrategy(3pm)	Abstract Removal Strategy interface for a Cache.
Cache::RemovalStrategy::FIFO(3pm)	FIFO Removal Strategy for a Cache.
Cache::RemovalStrategy::LRU(3pm)	LRU Removal Strategy for a Cache.
Cache::SharedMemoryBackend(3pm)	…
Cache::SharedMemoryCache(3pm)	…
Cache::Simple::TimedExpiry(3pm)	Simple, time-expiring cache.
Cache::SizeAwareCache(3pm)	…
Cache::SizeAwareCacheTester(3pm)	…
Cache::SizeAwareFileCache(3pm)	…
Cache::SizeAwareMemoryCache(3pm)	…
Cache::SizeAwareSharedMemoryCache(3pm)	…
Cache::Tester(3pm)	Test utility for Cache implementations.
caff(1)	Fire and Forget.
Cairo(3pm)	Perl interface to the cairo 2d vector graphics library.
Cairo::GObject(3pm)	Integrate Cairo into the Glib type system.
Cal::DAV(3pm)	A CalDAV client.
Calendar::Simple(3pm)	Perl extension to create simple calendars.
CAM::PDF(3pm)	PDF manipulation library.
CAM::PDF::Content(3pm)	PDF page layout parser.
CAM::PDF::Decrypt(3pm)	PDF security helper.
CAM::PDF::GS(3pm)	PDF graphic state.
CAM::PDF::GS::NoText(3pm)	PDF graphic state.
CAM::PDF::Node(3pm)	PDF element.
CAM::PDF::PageText(3pm)	Extract text from PDF page tree.
CAM::PDF::Renderer::Dump(3pm)	Print the graphic state of each node.
CAM::PDF::Renderer::Images(3pm)	Find all of the images in a page.
CAM::PDF::Renderer::Text(3pm)	Render an ASCII image of a PDF page.
CAM::PDF::Renderer::TextFB(3pm)	Framebuffer for CAM::PDF::Renderer::Text.
Canary::Stability(3pm)	Canary to check perl compatibility for schmorp's modules.
Captcha::reCAPTCHA(3pm)	A Perl implementation of the reCAPTCHA API.
Capture::Tiny(3pm)	Capture STDOUT and STDERR from Perl, XS or external programs.
Carp::Always(3pm)	Warns and dies noisily with stack backtraces.
Carp::Assert(3pm)	Executable comments.
Carp::Assert::More(3pm)	Convenience wrappers around Carp::Assert.
Carp::Clan(3pm)	Report errors from perspective of caller of a "clan" of modules.
Carp::Clan::Share(3pm)	Share your Carp::Clan settings with your whole Clan.
Carp::Datum(3pm)	Debugging And Tracing Ultimate Module.
Carp::Datum::Assert(3pm)	Assertion expression extractor.
Carp::Datum::Cfg(3pm)	Dynamic Debug Configuration Setting for Datum.
Carp::Datum::Flags(3pm)	Flag Constants.
Carp::Datum::MakeMaker(3pm)	Offer to strip Carp::Datum calls statically.
Carp::Datum::Strip(3pm)	Strips most Carp::Datum calls lexically.
Carp::Fix::1_25(3pm)	Smooth over incompatible changes in Carp 1.25.
Carton(3pm)	Perl module dependency manager (aka Bundler for Perl).
Carton::Doc::Bundle(3pm)	Bundle cached tarballs in vendor/cache.
Carton::Doc::Check(3pm)	Check if your cpanfile and local environment are in sync.
Carton::Doc::Exec(3pm)	Execute your script in a carton local environment.
Carton::Doc::FAQ(3pm)	Frequently Asked Questions.
Carton::Doc::Fatpack(3pm)	Fatpack carton executable into vendor/bin.
Carton::Doc::Install(3pm)	Install the dependencies.
Carton::Doc::List(3pm)	List dependencies tracked in the cpanfile.snapshot file.
Carton::Doc::Show(3pm)	Show the module information.
Carton::Doc::Tree(3pm)	Show the tree of dependency graph.
Carton::Doc::Update(3pm)	Update the dependencies.
Carton::Doc::Upgrading(3pm)	Upgrading document.
Carton::Doc::Version(3pm)	Display version.
Catalyst(3pm)	The Elegant MVC Web Application Framework.
catalyst.pl(1p)	Bootstrap a Catalyst application.
Catalyst::Action(3pm)	Catalyst Action.
Catalyst::Action::Deserialize(3pm)	Deserialize Data in a Request.
Catalyst::Action::DeserializeMultiPart(3pm)	Deserialize Data in a Multipart Request.
Catalyst::Action::RenderView(3pm)	Sensible default end action.
Catalyst::Action::REST(3pm)	Automated REST Method Dispatching.
Catalyst::Action::REST::ForBrowsers(3pm)	Automated REST Method Dispatching that Accommodates Browsers.
Catalyst::Action::Role::ACL(3pm)	Deprecated user role-based authorization action class.
Catalyst::Action::Serialize(3pm)	Serialize Data in a Response.
Catalyst::Action::Serialize::Data::Serializer(3pm)	Serialize with Data::Serializer.
Catalyst::Action::SerializeBase(3pm)	Base class for Catalyst::Action::Serialize and.
Catalyst::ActionChain(3pm)	Chain of Catalyst Actions.
Catalyst::ActionContainer(3pm)	Catalyst Action Container.
Catalyst::ActionRole::ACL(3pm)	User role-based authorization action class.
Catalyst::ActionRole::CheckTrailingSlash(3pm)	Test URI path for trailing slash and redirect if needed.
Catalyst::ActionRole::ConsumesContent(3pm)	Match on HTTP Request Content-Type.
Catalyst::ActionRole::HTTPMethods(3pm)	Match on HTTP Methods.
Catalyst::ActionRole::NeedsLogin(3pm)	Checks if a user is logged in and if not redirects him to login page.
Catalyst::ActionRole::NoSSL(3pm)	Force an action to be plain.
Catalyst::ActionRole::QueryMatching(3pm)	Match on GET parameters using type constraints.
Catalyst::ActionRole::RequireSSL(3pm)	Force an action to be secure only.
Catalyst::ActionRole::RequireSSL::Role(3pm)	Roles.
Catalyst::ActionRole::Scheme(3pm)	Match on HTTP Request Scheme.
Catalyst::Authentication::Credential::Authen::Simple(3pm)	Verify credentials with the Authen::Simple framework.
Catalyst::Authentication::Credential::HTTP(3pm)	HTTP Basic and Digest authentication for Catalyst.
Catalyst::Authentication::Credential::NoPassword(3pm)	Authenticate a user without a password.
Catalyst::Authentication::Credential::Password(3pm)	Authenticate a user with a password.
Catalyst::Authentication::Credential::Remote(3pm)	Let the webserver (e.g. Apache) authenticate Catalyst.
Catalyst::Authentication::Realm(3pm)	Base class for realm objects.
Catalyst::Authentication::Realm::Compatibility(3pm)	Compatibility realm object.
Catalyst::Authentication::Realm::Progressive(3pm)	Authenticate against multiple realms.
Catalyst::Authentication::Realm::SimpleDB(3pm)	A simplified Catalyst authentication configurator.
Catalyst::Authentication::Store(3pm)	All about authentication stores.
Catalyst::Authentication::Store::DBIx::Class(3pm)	A storage class for Catalyst Authentication using DBIx::Class.
Catalyst::Authentication::Store::DBIx::Class::User(3pm)	The backing user class for the.
Catalyst::Authentication::Store::Htpasswd(3pm)	Authen::Htpasswd based user storage/authentication.
Catalyst::Authentication::Store::Htpasswd::User(3pm)	A user object representing an entry in an htpasswd file.
Catalyst::Authentication::Store::IMAP(3pm)	Authentication store accessing an IMAP server.
Catalyst::Authentication::Store::IMAP::User(3pm)	An authentication user for IMAP.
Catalyst::Authentication::Store::Minimal(3pm)	Minimal authentication store.
Catalyst::Authentication::Store::Null(3pm)	Null authentication store.
Catalyst::Authentication::User(3pm)	Base class for user objects.
Catalyst::Authentication::User::Hash(3pm)	An easy authentication user object based on hashes.
Catalyst::Base(3pm)	Deprecated base class.
Catalyst::ClassData(3pm)	Class data accessors.
Catalyst::Component(3pm)	Catalyst Component Base Class.
Catalyst::Component::ApplicationAttribute(3pm)	Moose Role for components which capture the application context.
Catalyst::Component::ContextClosure(3pm)	Moose Role for components which need to close over the $ctx, without.
Catalyst::Component::InstancePerContext(3pm)	Return a new instance a component on each request.
Catalyst::Contributing(3pm)	…
Catalyst::Controller(3pm)	Catalyst Controller base class.
Catalyst::Controller::ActionRole(3pm)	(DEPRECATED) Apply roles to action instances.
Catalyst::Controller::FormBuilder(3pm)	Catalyst FormBuilder Base Controller.
Catalyst::Controller::HTML::FormFu(3pm)	Catalyst integration for HTML::FormFu.
Catalyst::Controller::REST(3pm)	A RESTful controller.
Catalyst::Controller::SRU(3pm)	Dispatch SRU methods with Catalyst.
Catalyst::Delta(3pm)	Overview of changes between versions of Catalyst.
Catalyst::Devel(3pm)	Catalyst Development Tools.
Catalyst::Dispatcher(3pm)	The Catalyst Dispatcher.
Catalyst::DispatchType(3pm)	DispatchType Base Class.
Catalyst::DispatchType::Chained(3pm)	Path Part DispatchType.
Catalyst::DispatchType::Default(3pm)	Default DispatchType.
Catalyst::DispatchType::Index(3pm)	Index DispatchType.
Catalyst::DispatchType::LocalRegex(3pm)	LocalRegex DispatchType.
Catalyst::DispatchType::LocalRegexp(3pm)	LocalRegexp DispatchType.
Catalyst::DispatchType::Path(3pm)	Path DispatchType.
Catalyst::DispatchType::Regex(3pm)	Regex DispatchType.
Catalyst::DispatchType::Regexp(3pm)	Regex DispatchType.
Catalyst::Engine(3pm)	The Catalyst Engine.
Catalyst::Engine::Apache(3pm)	Catalyst Apache Engines.
Catalyst::Engine::Apache2(3pm)	Base class for Apache 1.99x and 2.x Engines.
Catalyst::Engine::Apache2::MP19(3pm)	Catalyst Apache2 mod_perl 1.99x Engine.
Catalyst::Engine::Apache2::MP20(3pm)	Catalyst Apache2 mod_perl 2.x Engine.
Catalyst::Engine::Apache::MP13(3pm)	Catalyst Apache mod_perl 1.3x Engine.
Catalyst::Engine::HTTP(3pm)	Removed module.
Catalyst::EngineLoader(3pm)	The Catalyst Engine Loader.
Catalyst::Exception(3pm)	Catalyst Exception Class.
Catalyst::Exception::Basic(3pm)	Basic Catalyst Exception Role.
Catalyst::Exception::Detach(3pm)	Exception for redispatching using $ctx->detach().
Catalyst::Exception::Go(3pm)	Exception for redispatching using $ctx->go().
Catalyst::Exception::Interface(3pm)	Role defining the interface for Catalyst exceptions.
Catalyst::Helper(3pm)	Bootstrap a Catalyst application.
Catalyst::Helper::HTML::FormFu(3pm)	Helper to deploy HTML::FormFu template files.
Catalyst::Helper::Model::Adaptor(3pm)	Helper for the incredibly lazy.
Catalyst::Helper::Model::CDBI(3pm)	Helper for CDBI Models.
Catalyst::Helper::Model::DBI(3pm)	Helper for DBI Models.
Catalyst::Helper::Model::DBIC::Schema(3pm)	Helper for DBIC Schema Models.
Catalyst::Helper::Model::Factory(3pm)	Helper for the incredibly lazy.
Catalyst::Helper::Model::Factory::PerRequest(3pm)	Helper for the incredibly lazy.
Catalyst::Helper::View::Email(3pm)	Helper for Email Views.
Catalyst::Helper::View::Email::Template(3pm)	Helper for Templated Email Views.
Catalyst::Helper::View::Excel::Template::Plus(3pm)	Helper Class for Catalyst::View::Excel::Template::Plus.
Catalyst::Helper::View::JSON(3pm)	Helper for JSON Views.
Catalyst::Helper::View::Mason(3pm)	Helper for Mason Views.
Catalyst::Helper::View::PDF::Reuse(3pm)	Helper for PDF::Reuse Views.
Catalyst::Helper::View::Petal(3pm)	Helper for Petal Views.
Catalyst::Helper::View::TT(3pm)	Helper for TT Views.
Catalyst::Helper::View::TTSite(3pm)	Helper for TT view which builds a skeleton web site.
Catalyst::Log(3pm)	Catalyst Log Class.
Catalyst::Log::Log4perl(3pm)	DEPRECATED (see Log::Log4perl::Catalyst).
Catalyst::Manual(3pm)	The Catalyst developer's manual.
Catalyst::Manual::About(3pm)	The philosophy of Catalyst.
Catalyst::Manual::Actions(3pm)	Catalyst Reusable Actions.
Catalyst::Manual::CatalystAndMoose(3pm)	How Catalyst 5.8+ and Moose relate.
Catalyst::Manual::Components(3pm)	Reuseable components for Catalyst applications.
Catalyst::Manual::Cookbook(3pm)	Cooking with Catalyst.
Catalyst::Manual::Deployment(3pm)	Deploying Catalyst.
Catalyst::Manual::Deployment::Apache::FastCGI(3pm)	Deploying Catalyst with FastCGI on Apache.
Catalyst::Manual::Deployment::Apache::mod_perl(3pm)	Deploying Catalyst with mod_perl.
Catalyst::Manual::Deployment::DevelopmentServer(3pm)	Development server deployment.
Catalyst::Manual::Deployment::FastCGI(3pm)	Deploying Catalyst with FastCGI.
Catalyst::Manual::Deployment::IIS::FastCGI(3pm)	Deploying Catalyst with Microsoft IIS.
Catalyst::Manual::Deployment::lighttpd::FastCGI(3pm)	Deploying Catalyst with lighttpd.
Catalyst::Manual::Deployment::nginx::FastCGI(3pm)	Deploying Catalyst with nginx.
Catalyst::Manual::Deployment::SharedHosting(3pm)	Deploying Catalyst on Shared Hosting.
Catalyst::Manual::DevelopmentProcess(3pm)	Administrative structure of the Catalyst Development Process.
Catalyst::Manual::ExtendingCatalyst(3pm)	Extending The Framework.
Catalyst::Manual::Internals(3pm)	Catalyst Internals.
Catalyst::Manual::Intro(3pm)	Introduction to Catalyst.
Catalyst::Manual::Tutorial(3pm)	Catalyst Tutorial: Overview.
Catalyst::Manual::Tutorial::01_Intro(3pm)	Catalyst Tutorial - Chapter 1: Introduction.
Catalyst::Manual::Tutorial::02_CatalystBasics(3pm)	Catalyst Tutorial - Chapter 2: Catalyst Application.
Catalyst::Manual::Tutorial::03_MoreCatalystBasics(3pm)	Catalyst Tutorial - Chapter 3: More Catalyst Application.
Catalyst::Manual::Tutorial::04_BasicCRUD(3pm)	Catalyst Tutorial - Chapter 4: Basic CRUD.
Catalyst::Manual::Tutorial::05_Authentication(3pm)	Catalyst Tutorial - Chapter 5: Authentication.
Catalyst::Manual::Tutorial::06_Authorization(3pm)	Catalyst Tutorial - Chapter 6: Authorization.
Catalyst::Manual::Tutorial::07_Debugging(3pm)	Catalyst Tutorial - Chapter 7: Debugging.
Catalyst::Manual::Tutorial::08_Testing(3pm)	Catalyst Tutorial - Chapter 8: Testing.
Catalyst::Manual::Tutorial::09_AdvancedCRUD(3pm)	Catalyst Tutorial - Chapter 9: Advanced CRUD.
Catalyst::Manual::Tutorial::09_AdvancedCRUD::09_FormBuilder(3pm)	Catalyst Tutorial - Chapter 9: Advanced CRUD -.
Catalyst::Manual::Tutorial::09_AdvancedCRUD::09_FormFu(3pm)	Catalyst Tutorial - Chapter 9: Advanced CRUD - FormFu.
Catalyst::Manual::Tutorial::09_AdvancedCRUD::09_FormHandler(3pm)	Catalyst Tutorial - Chapter 9: Advanced CRUD -.
Catalyst::Manual::Tutorial::10_Appendices(3pm)	Catalyst Tutorial - Chapter 10: Appendices.
Catalyst::Manual::WritingPlugins(3pm)	DEPRECATED, see Catalyst::Manual::ExtendingCatalyst instead.
Catalyst::Middleware::Stash(3pm)	The Catalyst stash - in middleware.
Catalyst::Model(3pm)	Catalyst Model base class.
Catalyst::Model::Adaptor(3pm)	Use a plain class as a Catalyst model.
Catalyst::Model::Adaptor::Base(3pm)	Internal base class for Catalyst::Model::Adaptor and friends.
Catalyst::Model::CDBI(3pm)	[DEPRECATED] CDBI Model Class.
Catalyst::Model::CDBI::CRUD(3pm)	CRUD CDBI Model Class.
Catalyst::Model::DBI(3pm)	DBI Model Class.
Catalyst::Model::DBIC::Schema(3pm)	DBIx::Class::Schema Model Class.
Catalyst::Model::Factory(3pm)	Use a plain class as a Catalyst model, instantiating it every time it is requested.
Catalyst::Model::Factory::PerRequest(3pm)	Use a plain class as a Catalyst model, instantiating it once per.
Catalyst::Plugin::Authentication(3pm)	Infrastructure plugin for the Catalyst authentication framework.
Catalyst::Plugin::Authentication::Credential::OpenID(3pm)	OpenID credential for Catalyst::Auth framework.
Catalyst::Plugin::Authentication::Credential::Password(3pm)	Compatibility shim.
Catalyst::Plugin::Authentication::Internals(3pm)	All about authentication Stores and Credentials.
Catalyst::Plugin::Authentication::Store::Minimal(3pm)	Compatibility shim.
Catalyst::Plugin::Authentication::User(3pm)	Compatibility shim.
Catalyst::Plugin::Authentication::User::Hash(3pm)	Compatibility shim.
Catalyst::Plugin::Authorization::ACL(3pm)	ACL support for Catalyst applications.
Catalyst::Plugin::Authorization::ACL::Engine(3pm)	The backend that computes ACL checks for.
Catalyst::Plugin::Authorization::Roles(3pm)	Role based authorization for Catalyst based on.
Catalyst::Plugin::Cache(3pm)	Flexible caching support for Catalyst.
Catalyst::Plugin::Cache::Backend(3pm)	Bare minimum backend interface.
Catalyst::Plugin::Cache::Backend::FastMmap(3pm)	A thin wrapper for Cache::FastMmap that can handle non refs.
Catalyst::Plugin::Cache::Backend::Memory(3pm)	Stupid memory based caching backend.
Catalyst::Plugin::Cache::Choose::KeyRegexes(3pm)	Choose a cache backend based on key regexes.
Catalyst::Plugin::Cache::Curried(3pm)	Curried versions of "cache_set", "cache_get" and "cache_remove" that look.
Catalyst::Plugin::Cache::Store(3pm)	How to write a Cache store plugin.
Catalyst::Plugin::Cache::Store::FastMmap(3pm)	DEPRECATED - FastMmap cache store for Catalyst::Plugin::Cache.
Catalyst::Plugin::Cache::Store::Memory(3pm)	Stupid memory based cache store plugin.
Catalyst::Plugin::Captcha(3pm)	Create and validate Captcha for Catalyst.
Catalyst::Plugin::Compress(3pm)	Compress response.
Catalyst::Plugin::ConfigLoader(3pm)	Load config files of various types.
Catalyst::Plugin::ConfigLoader::Manual(3pm)	Guide to using the ConfigLoader plugin.
Catalyst::Plugin::CustomErrorMessage(3pm)	Catalyst plugin to have more "cute" error message.
Catalyst::Plugin::FillInForm(3pm)	FillInForm for Catalyst.
Catalyst::Plugin::I18N(3pm)	I18N for Catalyst.
Catalyst::Plugin::I18N::Manual(3pm)	(Draft) I18N and L10N with Catalyst and Template Toolkit.
Catalyst::Plugin::Log::Dispatch(3pm)	Log module of Catalyst that uses Log::Dis