table of contents
other versions
- stretch 2.3.1+dfsg-4
- testing 2.4.0+dfsg-11
- stretch-backports 2.4.0+dfsg-11~bpo9+1
- unstable 2.4.0+dfsg-11
PAIR_ALIGN(1) | User Commands | PAIR_ALIGN(1) |
NAMEΒΆ
pair_align - Pairwise alignmentSYNOPSIS
- 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-check BOOL
- Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
--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.
VERSION
- Last update: pair_align version: 1.3.6 [tarball] SeqAn version: 2.3.1
June 2017 | pair_align 2.3.1+dfsg-4 |