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halPhyloPTrain.py fails with hal2mafMP.py error #328

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@brantfaircloth

Running halPhyloPTrain.py fails (in cactus-v3.1.2 container) because it is trying to call hal2mafMP.py, which is reported as deprecated. Instead, it appears that in L57 halPhyloPTrain.py should be calling cactus-hal2maf.

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