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

[Juan Antonio Balbuena]

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. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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