Beast tree loading

[marybarker]

We would like to add Beast output (nexus) files to the repertoire of input formats that larch-usher accepts. This format is overall straightforward, with the caveats that the macros should be case insensitive.

Here is a site that shows several simple Beast output Nexus files.

The most complicated part will be parsing the trees presented in newick format in the Begin Trees block.

[marybarker]

The trees we would load would have sequences associated to their leaf nodes, but would not have sequences for ancestral states, so we will have to implement

• a method to assign compatible disambiguated edge mutations to the pendant edges, and possibly
• some form of Sankoff, or at least assign a single fixed sequence to all internal nodes to be optimized by matOptimize's built-in Fitch-Sankoff routine