Remove simulations
Cleanup
README update
Edge case
Pull in phyml
Support install
Fix test compile target and script
Merge pull request #1 from bcclaywell/dev

Fix test compile target and script
lcfit-compare build fix
Back to simulation

* Generate trees on the fly
* Modernize plotting code
Merge remote-tracking branch 'fhcrc/master' into sims

Conflicts:
	example/plot_fits.R
	sims/SConstruct
	sims/aggregate.R