Cyntenator is a software for identification of conserved syntenic blocks between multiple genomes. The program computes Smith-Waterman alignments of sequences, whereby the alphabet consists of all annotated genes and the scoring system is defined by protein sequence similarities and distances between species in a phylogenetic tree. The algorithm is an extension of the Syntenator partial order aligner, described in Rödelsperger and Dieterich, 2008.

AVAILABILITY

The source code and sample files can be downloaded at the FTP site: http://ftp.bioinformatics.org/pub/cyntenator/