Simulating multi allele gene trees from sample species tree

[Sourya Bhattacharyya]

Hello,

I am currently studying about the gene / species tree discordance due to duplication - loss - coalescent model, and want to generate multi allele gene trees from a sample species tree.

For example, let the model species tree be ((a,b),(c,d)), and a simulated multi-allele gene tree may be (((a1,a2),b1),(b2,((c,d1),d2))).
Here, a1, a2 are alleles of the taxon a. Similarly d1, d2 are alleles of the taxon d.

Is there any function / module in Dendropy by which I can generate such trees?

Thanks,
Sourya

[Jeet Sukumaran]

http://dendropy.org/primer/treesims.html#simulating-the-distribution-of-number-deep-coalescences-under-different-phylogeographic-history-scenarios

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