[R-sig-phylo] Substitution model for codon alignment

Hi All, I want to build a phylogenetic tree using codon alignment which is huge (280 MB). But there is no online information about suitable substitution models for codon alignment: is it HKY or GTR or any other? All the information available is about the substitution models for protein or

[R-sig-phylo] Negative transition rates in diversitree

Hi all I am fitting multitrait MuSSE models in the diversitree package to study correlated evolution between binary variables and some transition rates (qij) are negative. What is the meaning of negative transition rates? Thanks in advance Miguel Verdú --

[R-sig-phylo] simulate additive trees based on ultrametric trees

Hi all I am using core-gen (Keller-Schmidt et al. 2011 https://www.bioinf.uni-leipzig.de/Publications/PREPRINTS/11-013.pdf) to simulate host and parasite phylogenies. For each instance, a get a pair of ultrametric trees reflecting the coevolutionary history