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).