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ALTER-SEQUENCE-ALIGNMENT(1) - Linux man page online | User commands

Genomic sequences ALignment Transformation EnviRonment.

Chapter
September 2015
ALTER-SEQUENCE-ALIGNMENT(1) User Commands ALTER-SEQUENCE-ALIGNMENT(1)

NAME

alter-sequence-alignment - genomic sequences ALignment Transformation EnviRonment

SYNOPSIS

alter-sequence-alignment [option] [sequence]

DESCRIPTION

ALTER (ALignment Transformation EnviRonment) is a tool to transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

OPTIONS

-c (--collapse) Collapse sequences to haplotypes. -cg (--collapseGaps) Treat gaps as missing data when collapsing. -cl (--collapseLimit) N Connection limit (sequences differing at <= l sites will be collapsed) (default is l=0). -cm (--collapseMissing) Count missing data as differences when collapsing. -i (--input) FILE Input file. -ia (--inputAutodetect) Autodetect format (other input options are omitted). -if (--inputFormat) VAL Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR). -io (--inputOS) VAL Input operating system (Linux, MacOS or Windows) -ip (--inputProgram) VAL Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee). -o (--output) FILE Output file. -of (--outputFormat) VAL Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR). -ol (--outputLowerCase) Lowe case output. -om (--outputMatch) Output match characters. -on (--outputResidueNumbers) Output residue numbers (only ALN format). -oo (--outputOS) VAL Output operating system (Linux, MacOS or Windows). -op (--outputProgram) VAL Output program (jModelTest, MrBayes, PAML, PAUP, PhyML, ProtTest, RAxML, TCS, Cod‐ ABC, BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal , MAFFT, MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL) -os (--outputSequential) Sequential output (only NEXUS and PHYLIP formats).
alter-sequence-alignment 1.3.3 September 2015 ALTER-SEQUENCE-ALIGNMENT(1)
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