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.