What is Limes?

Limes is a free automated tool dedicated to perform exact comparisons of alternative taxonomies, whatever the methods or type of data-set involved to infer them. It is more especially adapted to compare taxonomic data-set composed by several species (typically at the genus level). To this end, Limes calculates four different indexes: Ctax, mCtax, Rtax (Miralles & Vences 2013) and the Match Ratio (Ahrens et al. 2016). Limes relies on a cladistic conceptual approach, and therefore assume that the species delimited by different methods represent monophyletic units.

Both Ctax and Match Ratio are intended to measure the agreement between two partitions, but their respective conceptual frameworks are fundamentally different. The Match Ratio is a direct measure of the partitions agreement (based on the ratio of identical subsets), whereas the Ctax is based on the hierarchical agreement between speciation events that are retrospectively deducted from the alternatives partitions.

How to cite us?

  • To cite Limes:

LIMES: A tool for comparing species partitions.
Jacques DUCASSE, Visotheary UNG, Guillaume LECOINTRE, Aurélien MIRALLES, 2019.

  • To cite the calculations of metrix (Rtax, Ctax):

Miralles A, Vences M (2013) New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards. PLoS ONE 8(7): e68242, http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068242

  • To cite the calculations of metrix Match ratio:

Dirk Ahrens, Tomochika Fujisawa, Hans-Joachim Krammer, Jonas Eberle, Silvia Fabrizi, Alfried P. Vogler; Rarity and Incomplete Sampling in DNA-Based Species Delimitation, Systematic Biology, Volume 65, Issue 3, 1 May 2016, Pages 478–494, https://doi.org/10.1093/sysbio/syw002