Simulating Gene Trees

Gene trees are generated from a pre-specified species tree under the multispecies coalescent model. The species tree is ultrametric with a molecular clock. The population size parameter theta's are specified by "#" in the species tree. 

An example species tree is given below in which the numbers immediately after # are population size parameters theta in the multispecies coalescent model. There is no need to specify theta for terminal branches unless multiple alleles are sampled from each species.

(((S1:0.1,S2:0.1):0.1#0.05,(S3:0.1,S4:0.1):0.1#0.05):0.01#0.05,S5:0.03)#0.05;


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Allowed types: sptree.
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