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.
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
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.