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 protected]>.
Benjamin Redelings.