Added T-node to remove a node; mapping codon sequences onto protein references now replaces stop codons with ---
GetInformation(*, tree) now returns the node->model map
Added timekeeping by phase to BranchSiteREL.bf
Added JSON reporting to BS-REL; removed PS tree rendering; added 3-rate BSREL compatibility option
Fixed rate class overcounting with traditional BS-REL; added version reporting to JSON
Fixed rate class overcounting with traditional BS-REL; added version reporting to JSON
Do not return infs and nans in getNodeOmegaDistribution for single rate classes
Include internal node names in PostOrderAVL2StringDistances to resolve internal branch name inconsistency with BranchSiteREL
Include internal node names in PostOrderAVL2StringDistances to resolve internal branch name inconsistency with BranchSiteREL
OK, BS-REL compatibility mode now works
removing unnecessary cmake files from gtest-1.7.0
fixes #206 Missing parameter in call to Parse function
Fixed an issue with not resetting paramter constraints in BranchSitREL following a convergence issue detection
Merge branch 'master' of github.com:veg/hyphy
Updated what is written to the JSON file by BranchSiteREL
MG94 c-aic written correctly
Added internal and leaf options as branch selectors; multiple testing correction uses the right number of conducted tests
Count the number of requested tests separately from the number of conducted tests
Fixed a bug when computeOnAGrid would not find a single point better than -inf and crash the analysis
Partial implementation of BUSTED (working name) using existing pieces of the new HBL library mock-up