Merge changes to BiallelicPatternProbabilityMatrix and likelihood functions from retic branch into dev branch. These changes should allow leaves to have no data for characters. These changes need to be tested after they are merged in; both to make sure nothing is broken and to add new tests to make sure the missing data are handled correctly. To merge them, run this from the dev branch:
git checkout retic -- src/ecoevolity/matrix.* src/ecoevolity/likelihood.*
Also, the BiallelicData class will need to be updated to allow characters for which one or more leaves have no data.