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pair_align: Pairwise alignment

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. 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 PAIR_ALIGN(1)

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