alignments-diff - Align two alignments for comparison.
alignments-diff alignment-file1 alignment-file2 [OPTIONS]
Align two alignments for comparison.
- -h, --help
- produce help message
- --alphabet arg
- set to 'Codons' to prefer codon alphabets
- Stack the two alignments into one alignment with duplicate names
- 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