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 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.