Langue: en

Version: 330870 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)


pair_align - Pairwise alignment


pair_align -s <FASTA sequence file> [Options]


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.


pair_align was written by Tobias Rausch.

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