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.