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Needs more work. Runtime is not significantly different from single threaded mode atm. Cols per second seem to slow toward end of the run for some reason. |
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I think the Biopython MSA data structure is not suitable for multithreaded processing. Try converting the alignment to a Polars dataframe before processing and then back to MSA afterwards. |
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Tested with numpy array as data structure. Speed is limited by complex dict lookups. RIP calculation step needs restructuring before multithreading will be useful. |
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Experimenting with multithreading of alignment processing.
*Did not end up using dask.