Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories

Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal of individual host-symbiont associations. We introduce Rtapas, an R package to perform Random Tanglegram Partitions. Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and internal nodes that maximize phylogenetic congruence. This new package extends the original implementation with a new algorithm that examines the contribution to phylogenetic incongruence of each host-symbiont association and adds ParaFit, a method designed to test for topological congruence between two phylogenies, to the list of global-..., , Supplementary Figures and Tables
SuppMat.pdf
Amphipod_trematode_example
Phylogenetic trees, association matrix and R script to perform the amphipod-trematode example
Amph_Trem.zip
Nuclear_organellar_example
Phylogenetic trees and R script to carry out the nuclear-organellar example in Orchids
Nucl_Plast.zip
Mamals_Fleas_example
Phylogenetic trees, association matrix and R script to carry out the mammals-fleas example 
Mam_Fleas.zip,