├── .gitignore ├── data ├── brpo │ ├── .param │ ├── .run │ ├── .trace │ ├── .treelist │ ├── brpo.ali │ └── brpo.tree └── moc │ ├── bikont.outgroup │ ├── calib │ ├── moc.ali │ └── moc.tree ├── pbManual4.1.pdf └── sources ├── .exrc ├── AmphiNode.h ├── BF.cpp ├── BPCompare.cpp ├── Bipartition.cpp ├── Bipartition.h ├── BipartitionList.cpp ├── BipartitionList.h ├── CVrep.cpp ├── Chain.cpp ├── Chain.h ├── Chrono.cpp ├── Chrono.h ├── Clock.cpp ├── Consensus.cpp ├── Consensus.h ├── Constants.h ├── MCParameters.cpp ├── MCParameters.h ├── Makefile ├── MaxLikelihood.cpp ├── Misc.cpp ├── Move.cpp ├── Node.h ├── PB.cpp ├── PhyloBayes.cpp ├── PhyloBayes.h ├── PhyloEM.cpp ├── PhyloProbs.cpp ├── PolyNode.cpp ├── PolyNode.h ├── PostPred.cpp ├── Pruning.cpp ├── Random.cpp ├── Random.h ├── ReadCV.cpp ├── ReadDiv.cpp ├── ReadSample.cpp ├── Sample.cpp ├── Sample.h ├── SampleSub.cpp ├── StopAfter.cpp ├── StopChain.cpp ├── SubMatrix.cpp ├── SubMatrix.h ├── SubSample.cpp ├── SumCV.cpp ├── TaxaParameters.cpp ├── TaxaParameters.h ├── TexTab.h ├── TraceComp.cpp ├── Tree.cpp ├── Tree.h ├── TreeList.cpp ├── TreeList.h ├── TreeToPS.cpp ├── correl.cpp ├── correlation.cpp ├── correlation.h ├── linalg.cpp ├── linalg.h ├── mystream.cpp ├── mystream.h ├── mystring.cpp ├── mystring.h └── phylo.h /.gitignore: -------------------------------------------------------------------------------- 1 | *.o 2 | *.d 3 | data/ 4 | -------------------------------------------------------------------------------- /data/brpo/.param: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/brpo/.param -------------------------------------------------------------------------------- /data/brpo/.run: -------------------------------------------------------------------------------- 1 | 1 2 | -------------------------------------------------------------------------------- /data/brpo/.trace: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/brpo/.trace -------------------------------------------------------------------------------- /data/brpo/.treelist: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/brpo/brpo.ali: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/brpo/brpo.ali -------------------------------------------------------------------------------- /data/brpo/brpo.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/brpo/brpo.tree -------------------------------------------------------------------------------- /data/moc/bikont.outgroup: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/moc/bikont.outgroup -------------------------------------------------------------------------------- /data/moc/calib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/moc/calib -------------------------------------------------------------------------------- /data/moc/moc.ali: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/moc/moc.ali -------------------------------------------------------------------------------- /data/moc/moc.tree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/data/moc/moc.tree -------------------------------------------------------------------------------- /pbManual4.1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/pbManual4.1.pdf -------------------------------------------------------------------------------- /sources/.exrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/.exrc -------------------------------------------------------------------------------- /sources/AmphiNode.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/AmphiNode.h -------------------------------------------------------------------------------- /sources/BF.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/BF.cpp -------------------------------------------------------------------------------- /sources/BPCompare.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/BPCompare.cpp -------------------------------------------------------------------------------- /sources/Bipartition.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Bipartition.cpp -------------------------------------------------------------------------------- /sources/Bipartition.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Bipartition.h -------------------------------------------------------------------------------- /sources/BipartitionList.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/BipartitionList.cpp -------------------------------------------------------------------------------- /sources/BipartitionList.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/BipartitionList.h -------------------------------------------------------------------------------- /sources/CVrep.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/CVrep.cpp -------------------------------------------------------------------------------- /sources/Chain.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Chain.cpp -------------------------------------------------------------------------------- /sources/Chain.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Chain.h -------------------------------------------------------------------------------- /sources/Chrono.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Chrono.cpp -------------------------------------------------------------------------------- /sources/Chrono.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Chrono.h -------------------------------------------------------------------------------- /sources/Clock.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Clock.cpp -------------------------------------------------------------------------------- /sources/Consensus.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Consensus.cpp -------------------------------------------------------------------------------- /sources/Consensus.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Consensus.h -------------------------------------------------------------------------------- /sources/Constants.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Constants.h -------------------------------------------------------------------------------- /sources/MCParameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/MCParameters.cpp -------------------------------------------------------------------------------- /sources/MCParameters.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/MCParameters.h -------------------------------------------------------------------------------- /sources/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Makefile -------------------------------------------------------------------------------- /sources/MaxLikelihood.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/MaxLikelihood.cpp -------------------------------------------------------------------------------- /sources/Misc.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Misc.cpp -------------------------------------------------------------------------------- /sources/Move.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Move.cpp -------------------------------------------------------------------------------- /sources/Node.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Node.h -------------------------------------------------------------------------------- /sources/PB.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PB.cpp -------------------------------------------------------------------------------- /sources/PhyloBayes.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PhyloBayes.cpp -------------------------------------------------------------------------------- /sources/PhyloBayes.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PhyloBayes.h -------------------------------------------------------------------------------- /sources/PhyloEM.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PhyloEM.cpp -------------------------------------------------------------------------------- /sources/PhyloProbs.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PhyloProbs.cpp -------------------------------------------------------------------------------- /sources/PolyNode.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PolyNode.cpp -------------------------------------------------------------------------------- /sources/PolyNode.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PolyNode.h -------------------------------------------------------------------------------- /sources/PostPred.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/PostPred.cpp -------------------------------------------------------------------------------- /sources/Pruning.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Pruning.cpp -------------------------------------------------------------------------------- /sources/Random.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Random.cpp -------------------------------------------------------------------------------- /sources/Random.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Random.h -------------------------------------------------------------------------------- /sources/ReadCV.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/ReadCV.cpp -------------------------------------------------------------------------------- /sources/ReadDiv.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/ReadDiv.cpp -------------------------------------------------------------------------------- /sources/ReadSample.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/ReadSample.cpp -------------------------------------------------------------------------------- /sources/Sample.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Sample.cpp -------------------------------------------------------------------------------- /sources/Sample.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Sample.h -------------------------------------------------------------------------------- /sources/SampleSub.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/SampleSub.cpp -------------------------------------------------------------------------------- /sources/StopAfter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/StopAfter.cpp -------------------------------------------------------------------------------- /sources/StopChain.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/StopChain.cpp -------------------------------------------------------------------------------- /sources/SubMatrix.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/SubMatrix.cpp -------------------------------------------------------------------------------- /sources/SubMatrix.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/SubMatrix.h -------------------------------------------------------------------------------- /sources/SubSample.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/SubSample.cpp -------------------------------------------------------------------------------- /sources/SumCV.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/SumCV.cpp -------------------------------------------------------------------------------- /sources/TaxaParameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TaxaParameters.cpp -------------------------------------------------------------------------------- /sources/TaxaParameters.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TaxaParameters.h -------------------------------------------------------------------------------- /sources/TexTab.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TexTab.h -------------------------------------------------------------------------------- /sources/TraceComp.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TraceComp.cpp -------------------------------------------------------------------------------- /sources/Tree.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Tree.cpp -------------------------------------------------------------------------------- /sources/Tree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/Tree.h -------------------------------------------------------------------------------- /sources/TreeList.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TreeList.cpp -------------------------------------------------------------------------------- /sources/TreeList.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TreeList.h -------------------------------------------------------------------------------- /sources/TreeToPS.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/TreeToPS.cpp -------------------------------------------------------------------------------- /sources/correl.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/correl.cpp -------------------------------------------------------------------------------- /sources/correlation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/correlation.cpp -------------------------------------------------------------------------------- /sources/correlation.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/correlation.h -------------------------------------------------------------------------------- /sources/linalg.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/linalg.cpp -------------------------------------------------------------------------------- /sources/linalg.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/linalg.h -------------------------------------------------------------------------------- /sources/mystream.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/mystream.cpp -------------------------------------------------------------------------------- /sources/mystream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/mystream.h -------------------------------------------------------------------------------- /sources/mystring.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/mystring.cpp -------------------------------------------------------------------------------- /sources/mystring.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/mystring.h -------------------------------------------------------------------------------- /sources/phylo.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bayesiancook/phylobayes/HEAD/sources/phylo.h --------------------------------------------------------------------------------