Provided by: bali-phy_3.6.1+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 arg 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 <email@example.com>.
Benjamin Redelings. Feb 2018 alignment-indices(1)