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.