LIMES, a tool for comparing species partition.

Motivation: Species delimitation (SD) is on the verge of becoming a fully fledged research field in systematics, but the variety of available approaches tends to result in significant-sometimes striking-incongruences, when tested comparatively with a given taxonomic sampling. Results: We present LIMES, an automatic calculation tool which qualitatively compares species partitions obtained by distinct SD approaches, regardless of their respective theoretical backgrounds, and even in absence of reference topology. The program implements four different previously published indexes, and allows their automated calculation.