pair_align1
Pairwise alignment
Usage
pair_align [OPTIONS]
-s
IN
Overview
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. |
Releases
8 releases since Debian 6.0 (Squeeze); the text changed 3 times.
--alphabet since Debian 10 (Buster);
--config since Debian 10 (Buster);
--gex since Debian 10 (Buster);
--gop since Debian 10 (Buster);
--help since Debian 10 (Buster);
--high since Debian 10 (Buster);
--low since Debian 10 (Buster);
--matrix since Debian 10 (Buster);
--method since Debian 10 (Buster);
--mmsc since Debian 10 (Buster);
--msc since Debian 10 (Buster);
--outfile since Debian 10 (Buster);
--seq since Debian 10 (Buster);
--version since Debian 10 (Buster);
-a since Debian 10 (Buster);
-c since Debian 10 (Buster);
-e since Debian 10 (Buster);
-g since Debian 10 (Buster);
-h since Debian 10 (Buster);
-hi since Debian 10 (Buster);
-lo since Debian 10 (Buster);
-m since Debian 10 (Buster);
-ma since Debian 10 (Buster);
-mm since Debian 10 (Buster);
-ms since Debian 10 (Buster);
-o since Debian 10 (Buster);
-s since Debian 10 (Buster).
-V until Debian 7 (Wheezy).