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.

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