https://github.com/dmulder/phylogen

As part of a graduate project I created the phylogen script, which combines the ASTRAL and IQTREE analysis tools into one iterative approach to finding the highest bootstrap score tree for various species of Mayflies. At the completion of the project, there was some work left undone, and I had a few ideas on how to improve the average bootstrap score of the final tree. For this hackweek, I'll complete the phylogen script by; first, calling the ASTRAL jar file in python using jpype, and second, creating python bindings to the IQTREE c code. Once these are complete, I hope that the script will run a bit faster, enabling me to run additional analysis on the mayfly genetic encoding data, and revealing a better tree.


Comments

  • dmulder
    4 months ago by dmulder | Reply

    I've completed the jpype work, and now I'm working on the iqtree python bindings.

  • dmulder
    4 months ago by dmulder | Reply

    Today I finished the iqtree python bindings. It currently works on a single node with multiple cores. Next I need to enable multi-node processing with MPI (it already has some MPI code, but needs reworked to use the latest changes).

  • dmulder
    4 months ago by dmulder | Reply

    Enabled multi-node using mpi4py MPIPoolExecutor. This works effectively the same as multiprocessing.Pool (which I was already using for single node processing). Need to add some intelligence around picking the best exon lengths, otherwise the cluster exhausts all available memory running multiple instances of ASTRAL!

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