NAME

       alignment-indices  -  Show  the  alignment  in terms of the index of each character in its
       sequence.

SYNOPSIS

       alignment-indices alignment-file [OPTIONS]

DESCRIPTION

       Show the alignment in terms of the index of each character in its sequence.

ALLOWED OPTIONS:

       -h, --help
              produce help message

       --align arg
              file with sequences and initial alignment

       --alphabet arg
              set to 'Codons' to prefer codon alphabets

       -c arg, --columns arg

              Ranges of columns to keep, like: 1-10,30-
       --invariant arg
              print only sites where this site and arg neighbors are invariant.

       --differences arg
              how many sequences may differ from the majority?

       --avoid-gaps arg (=3)
              How far from a gap must a column be to be invariant?

       --min-constraints arg
              Minimum # of constraints per column for a constraint to be emitted

REPORTING BUGS:

       BAli-Phy online help: <http://www.bali-phy.org/docs.php>.

       Please send bug reports to <bali-phy-users@googlegroups.com>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                        alignment-indices(1)