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pair_align

NAME

pair_align - Pairwise alignment

SYNOPSIS

pair_align -s <FASTA sequence file> [Options]

DESCRIPTION

Pairwise alignment - PairAlign

-h, --help

displays this help message

-V, --version

print version information

Main Options:

-s, --seq <FASTA Sequence File>

file with 2 sequences

-a, --alphabet [protein | dna | rna]

sequence alphabet (default protein)

-m, --method [nw, gotoh, sw, lcs]

alignment method (default gotoh) nw = Needleman-Wunsch gotoh = Gotoh sw = Smith-Waterman lcs = Longest common subsequence

-o, --outfile <Filename>

output filename (default out.fasta)

-f, --format [fasta | msf]

output format (default fasta)

Scoring Options:

-g, --gop <Int>

gap open penalty (default -11)

-e, --gex <Int>

gap extension penalty (default -1)

-ma, --matrix <Matrix file>

score matrix (default Blosum62)

-ms, --msc <Int>

match score (default 5)

-mm, --mmsc <Int>

mismatch penalty (default -4)

Banded Alignment Options:

-lo, --low <Int>

lower diagonal

-hi, --high <Int>

upper diagonal

DP Matrix Configuration Options:

-c, --config [ffff | ... | tttt]

alignment configuration (default ffff) tfff = First row with 0's ftff = First column with 0's fftf = Search last column for max ffft = Search last row for max All combinations are allowed.

AUTHOR

pair_align was written by Tobias Rausch.

This manual page was generated using html2man and polished by Soeren Sonnenburg <sonne@debian.org>, for the Debian project (but may be used by others).