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