table of contents
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, CodABC, 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).
September 2015 | alter-sequence-alignment 1.3.3 |