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                                           
P.O. Box 22085                                                   
46071 Valencia, Spain

j.a.balbu...@uv.es    tel. +34 963 543 658    fax +34 963 543 733

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