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>.

AUTHORS

       Benjamin Redelings.

                                                    Feb 2018                          alignment-chop-internal(1)