NAME

       pair_align - Pairwise alignment

       SYNOPSIS

              pair_align [OPTIONS] -s IN.fa

       DESCRIPTION

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

       -h, --help

              Displays this help message.

       --version

              Display version information

              Main Options:

       -s, --seq IN.fa

              FASTA file with two sequences. Valid filetypes are: fasta and fa.

       -a, --alphabet ALPHABET

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

       -m, --method METHOD

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

       -o, --outfile OUT

              Output filename. Valid filetypes are: fa, fasta, and msf. Default: out.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.

       -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 CONF

              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.

       VERSION

              pair_align version: 1.1 Last update November 2012