[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 nucleotide sequences. If anyone has created a phylogenetic tree based on codon alignment, your help will be much appreciated. Many thanks for your attention. Kind regards, Ravneet ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[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 -- Centro de Investigaciones sobre Desertificacion (CSIC-UV-GV) Carretera Moncada - Náquera, Km. 4,5 Apartado Oficial 46113 Moncada (Valencia) Spain Tel +34 96 3424204 Fax +34 96 3424160 www.uv.es/verducam ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[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 of host and parasite taxa. I was wondering what is the best way to simulate gene trees (i.e. additive trees) preserving the topology of the ultrametric ones. I tried to simulate sequence evolution (1000 nucleotids) under the GTR +Γ evolution model, using phylosim, and reconstruct the phylogenies by ML and BI. The problem is that the resulting phylogenies differ from the original topologies. Any help will be much appreciated. Thank you very much for your attention. Juan A. Balbuena -- Dr. Juan A. Balbuena Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia http://www.uv.es/~balbuena P.O. Box 22085 http://www.uv.es/cophylpaco 46071 Valencia, Spain e-mail: j.a.balbu...@uv.es tel. +34 963 543 658 fax +34 963 543 733 NOTE! For shipments by EXPRESS COURIER use the following street address: C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
