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, 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).