Developing distance estimation on mismatched trees
dev-tree branch first commit
Developing pure dendropy implementation of Tree class, to remove need for tree manipulation utility finctions, which currently use dendropy anyway
Incremental update on tree_dendropy_subclass.py
Done: NNI and basic I/O + manipulations. To do: SPR and TreeGen functionality.
Done: TreeGen, reversible derootingand rooting. To Do: SPRs
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Added spr and rspr methods, and supporting methods, to Tree
TreeGen class methods added to Tree
Docstrings added to SPR related methods
Random LGT implemented in a `good enough` way (room for improvement in implementation, but correctness seems ok)
Merge branch 'dev'
Tidy up after merge