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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.
pair_align 1.3.7 [tarball]