NAME

alignment-chop-internal -- Remove ancestral sequences from an alignment.

SYNOPSIS

alignment-chop-internal [OPTIONS] < alignments-file

DESCRIPTION

Remove ancestral sequences from an alignment.

ALLOWED OPTIONS:

-h, --help
produce help message
--align arg
file with sequences and initial alignment
--alphabet arg
set to 'Codons' to prefer codon alphabets
--tree arg
file with tree that specifies leaves to keep
-N arg, --nleaves arg
number of sequences to keep

REPORTING BUGS:

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

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