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| PAIR_ALIGN(1) |
|
PAIR_ALIGN(1) |
NAME¶
pair_align - Pairwise alignment
SYNOPSIS¶
pair_align [OPTIONS] -s IN
DESCRIPTION¶
The program allows one to align two sequences using dyamic programming alignment
algorithms while tweaking various parameters.
OPTIONS¶
- -h, --help
- Display the help message.
- --version
- Display version information.
Main Options:¶
- -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.
Scoring Options:¶
- -g, --gop INTEGER
- Gap open penalty. Default: -11.
- -e, --gex INTEGER
- Gap extension penalty. Default: -1.
- -ma, --matrix STRING
- Score matrix.
- -ms, --msc INTEGER
- Match score. Default: 5.
- -mm, --mmsc INTEGER
- Mismatch penalty. Default: -4.
Banded Alignment Options:¶
- -lo, --low INTEGER
- Lower diagonal.
- -hi, --high INTEGER
- Upper diagonal.
DP Matrix Configuration Options:¶
- -c, --config STRING
- Alignment configuration. One of ffff, ffft, fftf,
fftt, ftff, ftft, fttf, fttt,
tfff, tfft, tftf, tftt, ttff,
ttft, tttf, and tttt.
ALIGNMENT CONFIGURATION¶
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.
