MASTER is extremely slow if requesting exact number of tips

ArtPoon / kamphir

Phylogenetic inference using a tree-shape kernel in an Approximate Bayesian Computation framework

BSD 3-Clause "New" or "Revised" License

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MASTER is extremely slow if requesting exact number of tips #16

Closed ArtPoon closed 9 years ago

ArtPoon commented 9 years ago

Since this is a forward-time simulation, it has to discard a great many simulations in order to generate a tree with a predefined number of tips. While it is not strictly necessary for trees being compared with the kernel function to have the same numbers of tips, I am worried that this may bias phylodynamic inference.

ArtPoon commented 9 years ago

Solution for now is set exact="false" in MASTER XML so that nLeaves gives the minimum number of tips, and then prune the tree with Biopython to the required number. Implemented as of commit a96393a.