pair_align - Pairwise alignment
pair_align [OPTIONS] -s IN
The program allows one to align two sequences using dyamic
programming alignment algorithms while tweaking various parameters.
- -h, --help
- Display the help message.
- --version
- Display version information.
- -s, --seq
INPUT_FILE
- FASTA file with two sequences. Valid filetypes are: .frn,
.fna, .ffn, .fasta, .faa, and .fa.
- -a, --alphabet
STRING
- Sequence alphabet. One of protein, dna, rna, and
text. Default: protein.
- -m, --method
STRING
- DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest
Common Subsequence One of nw, gotoh, sw, and
lcs. Default: gotoh.
- -o, --outfile
OUTPUT_FILE
- Output filename. Valid filetypes are: .msf, .frn,
.fna, .ffn, .fasta, .faa, and .fa.
Default: out.fasta.
- -c, --config
STRING
- Alignment configuration. One of ffff, ffft, fftf,
fftt, ftff, ftft, fttf, fttt,
tfff, tfft, tftf, tftt, ttff,
ttft, tttf, and tttt.
The alignment configuration is a string of four characters, each
being either t or f. All combinations are allowed. The meaning is as
follows.
- tfff
- First row initialized with 0s.
- ftff
- First column initialized with 0s.
- fftf
- Search last column for maximum.
- ffft
- Search last row for maximum.