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).