v5.1 [31 Jul 2012]
Sped up ML bootstrap tree construction (by avoiding likelihood computation at non-resampled sites).
Added TBR (Tree Bisection Reconnection) and SPR (Subtree Pruning Regrafting) search heuristics for MP phylogeny reconstruction.
Removed CNI (Close Neighbor Interchange) search heuristic from MP phylogeny reconstruction.
Replaced slow TIFF image export with PNG export (similar format, lossless, widely used).
Fixed a critical calculation bug which occured in some cases where bootstrapping wasn't resampled correctly (only was an issue with ML trees). This bug only ever existed in the beta.