alignment-indices1

Show the alignment in terms of the index of each character in its sequence.

Usage

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⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .

4 releases since Debian 10 (Buster); the text changed 2 times.