progressive gene order alignments
Cyntenator identifies 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.
