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.