HyPhy Documentation
: Standard Analyses
AnalyzeCodonData.bf
AnalyzeNucDataFreq.bf
AnalyzeNucProtData.bf
BranchSwap.bf
ClusterAnalysis.bf
CodonModelCompare.bf
ConvertDataFile.bf
LocalMolClock.bf
MergeSequences.bf
MergeSites.bf
MFPositiveSelection.bf
ModelTest.bf
MolecularClock.bf
MolClockAllRoots.bf
NeighborJoining.bf
NucModelCompare.bf
PairwiseRelativeRate.bf
PairwiseRelativeRatio.bf
PartitionDataFile.bf
PositiveSelection.bf
RelativeRate.bf
RelativeRatio.bf
SequentialAddition.bf
SlidingWindowAnalysis.bf
StarDecomposition.bf
TopologySearch.bf
TopologySearchConstrained.bf
UpperBound.bf
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002