Autoformatted code
Updated MANIFEST to include extensions
Make Concatenation object produce proper PLL qfile
Reinserted 3D plotting import
Changes to bin/treeCl adding a couple of convenience options
Merge branch 'master' of github.com:kgori/treeCl
Bug: mutable arguments in Class init
Updated gtp.jar
Updated gtp.jar to have EuclideanDistance and RobinsonFoulds
Refactored tree out of datastructs; removed trcl_tree
Refactored tree out of datastructs; removed trcl_tree
Made java classes from GTP available: treeCl.PhyloTree, treeCl.GTP
Java tree distances available
PLL based likelihood calculations
merged with master