alignment−indices

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 AT googlegroups DOT com>.

AUTHORS

Benjamin Redelings.