Provided by: bali-phy_3.3+dfsg-1_amd64
alignment-indices – Show the alignment in terms of the index of each character in its sequence.
alignment-indices alignment-file [OPTIONS]
Show the alignment in terms of the index of each character in its sequence.
-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
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <firstname.lastname@example.org>.
Benjamin Redelings. Feb 2018 alignment-indices(1)