Software for UNIX

Outline of Programs
aln Global alignment of a pair of DNA or protein sequences, or groups of sequences. Supports spliced alignment when one of the sequences is a genomic DNA sequence.
swg Local alignment of a pair of DNA or protein sequences by Smith-Waterman-Gotoh algorithm. Currently spliced alignment is not supported. Profile version is very slow.
prrn Global multiple alignment of a set of protein or DNA sequences by doubly nested iterative refinement method.
phyln UPGMA or NJ method to make a phylogenetic tree from a multiple alignment.
makmdm Construct binary PAM matrices. Must be run once before the first run of aln, swg or prrn.

The program codes below are copyrighted by Osamu Gotoh and Saitama Cancer Center.
  1. scc_soft2.5.2.tar.gz (last updated 1998.11)
  2. scc_soft3.0b.tar.gz (last updated 2001.3)
  3. README.3.0b

Note: Since version 3.0, programs for protein sequences (alp, psm, prrp, and phylp) have been merged to those for nucleotide sequences (aln, nsm, prrn, and phyln, respectively), and nsm was renamed as swg.


  1. Cytochrome P450 genes predicted from C. elegans genome


Parallel prrn

Note: Parallel prrn is a service provided by Human Genome Center of the University of Tokyo. The inner loop of the doubly nested iterations is executed in parallel with 32-64 CPUs. This parallelization, made possible by Y. Totoki, ensures fast convergence, although the accuracy of the resulting multiple sequence alignments is slightly reduced on average.