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).