Notes - xflouris/libpll GitHub Wiki

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  • pll_set_invariant_sites_proportion(...) cannot be called before initializing the tip states
  • each time the proportion of invariant sites is updated, it is also necessary to update the probability matrices: pll_update_prob_matrices(...)
  • We should take care when we implement the pattern compresion. If the proportion of invariable sites is set, that must be done after removing the duplicated sites.