SEQAlign implements three different algorithms for finding an optimal global alignment of two sequences:
SEQAlign is written in C, and should compile on any Unix system. Unpack
the source code (tar xvfz seqalign-X.Y.tar.gz), change
directory to the seqalign-X.Y/ directory and run
make. A seqalign executable will be built in
the bin/ subdirectory.
To use SEQAlign, an algorithm, score matrix and two sequences must be
specified. Optionally, linear or affine gap cost can be specified. See
seqalign --help for more details. Two example sequences
as well as score matrices are provided in the data/
directory. Example usage:
# bin/seqalign -l hirschberg -s data/editdist.phy data/human.seq data/mouse.seq Similarity = 1290
The optimal global alignment of two sequences can be outputted using
the -o[=FILE] option:
# bin/seqalign -o -l gotoh -s data/matrix.phy data/human.seq data/mouse.seq Similarity = 5643 >seq1 acggtaatgacaggaatct-ctcttaatctgcaactaggcacagagatgggccaatccaagaagggcgcggggatttttg a-at-t-ttcttgggt-c-caatagttggtggtct-gactctataaaagaagagtagctctttcctttc-ctccacagac gtctct-gcaggcaagcttttctgtg--gttttgcca-tggctcgtactaaacagac-agctcg-gaaatccaccgg-cg g-taaagcgccacgcaagcagctggctaccaaggctgctcgcaaga-gcgc-gccggctaccggcggtgtgaaaaagcct caccgttaccg-tccgggtactg-tggctctgcgtgagatccgccgctaccaaaagtcgaccgagttgctgattcg-gaa gctgccgttccagcgcctggt--gcgagaaatcgc-ccaagacttcaagaccgatct-tcgcttccagagctctg-cggt aatggcgctgcaggaggcttgtgaggcctacttggtagggct-ctttgaggacac-aaacct-ttgcgccatccatgcta agcgagtgactattatgcccaaagacatccagctcgctcgccgcattcgcggagaaagagcgtaaatgtaaagttactt- t---t-tcat-c-agtcttaaaacccaaaggctcttttcagagcca-cccac-ttattcca-acgaaagtagctgtgata attttttgttgtctcaa >seq2 a----aa-g---g----ctgc-cttg-tc--caa-t---ca--ga-a----c-a------g--gggtg------tcttt- atatata--c--gggtacg-aa-ag--g-----ctagact-t-t----------c-g-t-ttt--tt-cg-tc-a----- -t-t-tagcagg---g-ttt---a-gaagttc-gc-aatggctcgtaccaagcagact-gctcgc-aagtccac-gggtg gg-aaagcgccacgcaagcagctggccaccaaggctgctcg-aaaaagcgct-ccagccaccggcggcgtgaagaagccc caccgttaccggcccgg-cac-ggtggctctgcgcgagatccgccgctaccagaagtcgaccgagctgctgattcgcaaa -ctgccattccagcgtctagtccgtgaga--tcgcgc-aggacttcaagactgatctg-cgttttcagagctc-ggcggt gatggcgctgcaggaggcctgcgaggcctacctggtggggctg-tttgaggacaccaa-cctat-gcgccattcacgcca agcgagtgactatcatgcccaaggacatccagcttgctcgccgcattcgtggggagagggcgtaaat-t---gt--cttg tgaatgt-gtgctaacc--aaaacccaaaggctcttttcagagccaacc-acctt-ttctata--aaa--ag-t-tg-c- -------gt--------
SEQAlign uses the SEQIO package for reading and writing sequences.
Copyright (c) 1996 by James Knight at Univ. of California, Davis.