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

-h, –help
              produce help message

       –alignarg
              file with sequences and initial alignment

       –alphabetarg
              set to `Codons' to prefer codon alphabets

       -carg, –columnsarg

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

       –differencesarg
              how many sequences may differ from the majority?

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

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

       Benjamin Redelings.

                                                    Feb 2018                                alignment-indices(1)

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

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

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

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

alignment-indicesalignment-file [OPTIONS]