NAME
alignment-indices - Show the alignment in terms of the index of each character in its sequence.
SYNOPSIS
alignment-indices alignment-file [OPTIONS]
DESCRIPTION
Show the alignment in terms of the index of each character in its sequence.
ALLOWED OPTIONS:
- -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
REPORTING BUGS:
BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .
Please send bug reports to ⟨[email protected]⟩\c .
AUTHORS
Benjamin Redelings.