PAIR_ALIGN

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.