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

Genomic sequences ALignment Transformation EnviRonment.

September 2015


alter-sequence-alignment - genomic sequences ALignment Transformation EnviRonment


alter-sequence-alignment [option] [sequence]


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.


-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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