NAME

       pair_align - Pairwise alignment

SYNOPSIS

       pair_align [OPTIONS] -s IN

DESCRIPTION

       The  program  allows  one  to  align  two  sequences  using dyamic programming alignment algorithms while
       tweaking various parameters.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options:
       -s, --seq INPUT_FILE
              FASTA file with two sequences. Valid filetypes are: .frn, .fna, .ffn, .fasta, .faa, and .fa.

       -a, --alphabet STRING
              Sequence alphabet. One of protein, dna, rna, and text. Default: protein.

       -m, --method STRING
              DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common  Subsequence  One  of
              nw, gotoh, sw, and lcs. Default: gotoh.

       -o, --outfile OUTPUT_FILE
              Output  filename.  Valid  filetypes  are:  .msf, .frn, .fna, .ffn, .fasta, .faa, and .fa. Default:
              out.fasta.

   Scoring Options:
       -g, --gop INTEGER
              Gap open penalty. Default: -11.

       -e, --gex INTEGER
              Gap extension penalty. Default: -1.

       -ma, --matrix STRING
              Score matrix.

       -ms, --msc INTEGER
              Match score. Default: 5.

       -mm, --mmsc INTEGER
              Mismatch penalty. Default: -4.

   Banded Alignment Options:
       -lo, --low INTEGER
              Lower diagonal.

       -hi, --high INTEGER
              Upper diagonal.

   DP Matrix Configuration Options:
       -c, --config STRING
              Alignment configuration. One of ffff, ffft, fftf, fftt, ftff, ftft, fttf, fttt, tfff, tfft,  tftf,
              tftt, ttff, ttft, tttf, and tttt.

ALIGNMENT CONFIGURATION

       The  alignment  configuration  is a string of four characters, each being either t or f. All combinations
       are allowed. The meaning is as follows.

       tfff   First row initialized with 0s.

       ftff   First column initialized with 0s.

       fftf   Search last column for maximum.

       ffft   Search last row for maximum.

pair_align 1.3.8 [tarball]                                                                         PAIR_ALIGN(1)