PAIRALIGN(1)
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).