Modified runPhyML to randomly choose a subset of 3999 seqs if there are >= 4000, because that is the standard-compile hardcoded default for PhyML
Modified runPhyML to randomly choose a subset of 3999 seqs if there are >= 4000, because that is the standard-compile hardcoded default for PhyML

pedlefsen/hiv-founder-id,pedlefsen/hiv-founder-id,pedlefsen/hiv-founder-id