WABA
From BioPerl
Jim Kent's Wobble Aware Bulk Aligner for cross-species whole genome alignment [1]. This tool was seems to be optimally tuned for species at the distance of C. elegans ⇔ C. briggsae (≈100 Mya) [2].
References
- Kent WJ and Zahler AM. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res 2000 Aug; 10(8) 1115-25. pmid:10958630.
- Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, and Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 2003 Nov; 1(2) E45. doi:10.1371/journal.pbio.0000045 pmid:14624247.
