automatically performing branchlength-estimation step now. simplified main inference code, removed subprograms... major code simplification, unittests pass
implemented new logging scheme, much cleaner output, main program seems to work. Need to test on real data
further changes to logging output and minor things
added getStats.awk, minor bugfixes to generate_multihetsep
fixed linux makefile, added test run
some more command line parameters and better output
fixed definition of objective function
fixed bug in branchlength
simplified Makefiles, played around with the emission probs, not yet fixed
changed tTot to tLeaf, emission probability not right
minor
minor
fixed emission problem. Things work for M=4 and higher, but getting slightly off
implemented directed Emissions, not working yet
added readTreeFile option
m
m
fixed treeFileNames input and tweaked the emission probability a bit
makefile changes
merged Makefile.linux