The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots ("Navajo rugs") and (3) categorization of synapomorphies (using TNT) and automatic generation of diagnostic character-state plots. YBYRÁ also provides (4) a framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist).
NOTE: I changed the link to MSdist recently (July 17, 2017).
NEW: The new program ybyra_wild.py ranks terminals (all of them or the ones listed in a constraint text file) according to the number of combined clades in all topologies after the corresponding clade is removed. The strict consensus will have more politomies when number of combined clades is higher. Terminals that result in fewer combined clades when removed are more likely to be considered 'wildcards' or 'rogue taxa'.
There is now an image of Ubuntu 16.04 (64 bits) available for VirtualBox. The image (an approx. 4 GB .ova file) contains YBYRÁ with all of its dependencies already installed. Vist the website of the Laboratório de Anfíbios to know more.
How to cite the article
Machado D. J. (2015) YBYRÁ facilitates comparison of large phylogenetic trees. BMC Bioinformatics16: 204. doi: 10.1186/s12859-015-0642-9
How to cite the program available at our lab's website
Machado D. J. (2013). YBYRÁ - a fast and resourceful tool for examining clade prevalence in large sets of trees. XXXII Meeting of the Willi Hennig Society, Rostock, Germany. p. 140.
SOME PUBLISHED WORKS USING YBYRÁ
Marques F. P. de L. & Caira J. N. (2016) Pararhinebothroides - Neither the Sister-Taxon of Rhinebothroides Nor a Valid Genus. Journal of Parasitology102(2): 249-59. doi: 10.1645/15-894
Simon M. F., Pastore J. F. B., Souza A. F. et al. (2015) Molecular Phylogeny of Stryphnodendron (Mimosoideae, Leguminosae) and Generic Delimitations in the Piptadenia Group. International Journal of Plant Sciences177(1): 44-59. doi: 10.1086/684077
Grant G., Rada M., Anganoy-Criollo M. et al. (2017) Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea). South American Journal of Herpetology12(s1): S1-S90. Available here.
Example of a published cladogram using YBYRÁ for character categorization