p-matrix computations (theory + usage) and how pmatrix updates work (rate matrix specification for each rate category)
Document the PLL_ATTRIB_PATTERN_TIP attribute, and the various maps in the partition (charmap, tipmap, tipchars) and why they are needed for arbitrary number of states.
Update the wikis for conditional probabilities and log-likelihood computation. Document the per-site log-likelihood computation.
Explain how heterotachous/mixture models can be implemented
Document the following:
PLL_ATTRIB_PATTERN_TIPattribute, and the various maps in the partition (charmap, tipmap, tipchars) and why they are needed for arbitrary number of states.