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pair_align - Pairwise alignment


pair_align [OPTIONS] -s IN


The program allows one to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.


Display the help message.
Display version information.

Main Options:

FASTA file with two sequences. Valid filetypes are: .frn, .fna, .ffn, .fasta, .faa, and .fa.
Sequence alphabet. One of protein, dna, rna, and text. Default: protein.
DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence One of nw, gotoh, sw, and lcs. Default: gotoh.
Output filename. Valid filetypes are: .msf, .frn, .fna, .ffn, .fasta, .faa, and .fa. Default: out.fasta.

Scoring Options:

Gap open penalty. Default: -11.
Gap extension penalty. Default: -1.
Score matrix.
Match score. Default: 5.
Mismatch penalty. Default: -4.

Banded Alignment Options:

Lower diagonal.
Upper diagonal.

DP Matrix Configuration Options:

Alignment configuration. One of ffff, ffft, fftf, fftt, ftff, ftft, fttf, fttt, tfff, tfft, tftf, tftt, ttff, ttft, tttf, and tttt.


The alignment configuration is a string of four characters, each being either t or f. All combinations are allowed. The meaning is as follows.

First row initialized with 0s.
First column initialized with 0s.
Search last column for maximum.
Search last row for maximum.
pair_align 1.3.8 [tarball]