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
<bali-phy-users@googlegroups.com>.