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).
Version 1.0 (15. July 2009) ReviSeptember62009 PAIRALIGN(1)