Provided by: alter-sequence-alignment_1.3.4-6_all bug


       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

       -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).