table of contents
ALTER-SEQUENCE-ALIGNMENT(1) | User Commands | ALTER-SEQUENCE-ALIGNMENT(1) |
NAME¶
alter-sequence-alignment - genomic sequences ALignment Transformation EnviRonmentSYNOPSIS¶
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 |