chromosomes rate matrix and function working, need to work on phyloCTMC
ChromosomesState objecte
added chromosomes test script
ChromosomesDataReader
chromosomes up and running - needs testing on real data
bug fixes
fixes to chromosome state and start of ancestral state
changes to DNAState.cpp by Seabastian
added chromosome test scripts and data
RateMatrix_Chromosomes2 object uses eigensystem decomposition instead of repeated squaring - for likelihood calculation comparison tests
started work on AncestralStateMonitor object
cleaning up AncestralStateMonitor so it compiles
testing joint chromosomes/phylogeny infernce
removing debugging messages
added constraints to uniformTopology
added get topology function to RlBranchLengthTree
added Func_readBranchLengthTrees
fixed joint inference to use starting tree and constraints
basic AncestralStateMonitor working - still need marginal props updated
organizing AncestralStateMonitor::monitor