Built most of the functions needed to make cactus build trees for
genomes.
Completed basic code for building trees for blocks.
Adding memory cleanup for phylogeny.
Tidied up code for building trees.
All tests passing, but not performing well.
Adding extra logging to phylogeny building process to summarise.
Use longest outgroup branch to root tree
Merging in the development branch to the phylogeny branch, bringing in
the multiple outgroups code.
Oops, reenabling splitting.
Making code rely only on the tree partitioning process.
Reconciliation in, most stuff is probably broken
Fix all (?) species tree crashes
Fix cactus_setup failing to add sequence to ancestral outgroups
Fix cactus_setup for real this time
All tests pass
Fix (part of?) progressive tests

Single-node species trees were being generated
Fix the rest of progressive tests and add tree-building params
Fix subtree extraction for cactus2hal
Test whack-a-mole
Enforce binarizing of species trees even with ancestral outgroups.

There will be extra losses in some cases as a side effect.