WABA

Jim Kent's Wobble Aware Bulk Aligner for cross-species whole genome alignment waba. This tool was seems to be optimally tuned for species at the distance of C. elegans ⇔ C. briggsae (≈100 Mya) briggsae.

References

<biblio>

1. waba pmid=10958630
2. briggsae pmid=14624247

</biblio>