NAME
alignments-diff - Align two alignments for comparison.
SYNOPSIS
alignments-diff alignment-file1 alignment-file2 [OPTIONS]
DESCRIPTION
Align two alignments for comparison.
GENERAL OPTIONS:
- -h, –help
-
produce help message
INPUT OPTIONS:
- –alphabet arg
-
set to `Codons' to prefer codon alphabets
OUTPUT OPTIONS:
- –merge
-
Stack the two alignments into one alignment with duplicate names
- –dual
-
Write out the two aligned alignments separately
- –fill arg (=gap)
-
blank columns filled with: gap or unknown
- -d arg, –differences-file arg
-
Filename to store differences in AU format
- –blocksize arg (=20)
-
Width of blocks of same color
- –classes arg (=1)
-
Number of groups for non-matching characters
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.