Fixed bug causing phycas to complain that it could not find an outgroup taxon when in fact that outgroup taxon was in the tree
Changed color scheme used by the TreeViewer used for debugging likelihood calculations
Added yet another verbose UpdateAllUpdaters function to MCMCChainManager; this one saves debug info to a file
Changed debugShowTransformedRelativeRates to use stringstream rather than cerr, making it more flexible
This commit fixes bug 11 described in BUGS file
Fixes reference output for tests affected by Bug 11 described in the BUGS file