pair_align - Pairwise alignment

       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)

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

       pair_align - Pairwise alignment

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions:-s, --seqINPUT_FILE
              FASTA file with two sequences. Valid filetypes are: .frn, .fna, .ffn, .fasta, .faa, and .fa.

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

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

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

   ScoringOptions:-g, --gopINTEGER
              Gap open penalty. Default: -11.

       -e, --gexINTEGER
              Gap extension penalty. Default: -1.

       -ma, --matrixSTRING
              Score matrix.

       -ms, --mscINTEGER
              Match score. Default: 5.

       -mm, --mmscINTEGER
              Mismatch penalty. Default: -4.

   BandedAlignmentOptions:-lo, --lowINTEGER
              Lower diagonal.

       -hi, --highINTEGER
              Upper diagonal.

   DPMatrixConfigurationOptions:-c, --configSTRING
              Alignment configuration. One of ffff, ffft, fftf, fftt, ftff, ftft, fttf, fttt, tfff, tfft,  tftf,
              tftt, ttff, ttft, tttf, and tttt.

pair_align [OPTIONS] -sIN