Frith MC, Kawaguchi R.

Genome Biol. 2015 May 21;16:106. doi:10.1186/s13059-015-0670-9

Split-alignment of genomes finds orthologies more accurately.

Optimal set of local alignments. Striking example of intra-chromosomal loss of synteny between D. melanogaster and D. pseudoobscura. Heuristic approach inspired by the “repeated matches algorithm” of Durbin and coll., 1998.