I am using core-gen (Keller-Schmidt et al. 2011
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
Juan A. Balbuena
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