as.data.frame.simMat	simMat
as.matrix.simMat	simMat
as.simMat	simMat
as.simMat.matrix	simMat
as.simMat.vector	simMat
Behdenna.ProtWeaver	ProtWeaver-PAPreds
BlastSeqs	BlastSeqs
BlockExpansion	BlockExpansion
BlockReconciliation	BlockReconciliation
BuiltInEnsembles	BuiltInEnsembles
CIDist	PhyloDistance-CI
CIDist_NullDist	CIDist_NullDist
Coloc.ProtWeaver	ProtWeaver-ColocPreds
ContextTree.ProtWeaver	ProtWeaver-DMPreds
CorrGL.ProtWeaver	ProtWeaver-PAPreds
dendrapply	dendrapply
Diag	simMat
Diag.simMat	simMat
Diag<-	simMat
Diag<-.simMat	simMat
DisjointSet	DisjointSet
DPhyloStatistic	DPhyloStatistic
Endosymbionts_GeneCalls	Endosymbionts_GeneCalls
Endosymbionts_LinkedFeatures	Endosymbionts_LinkedFeatures
Endosymbionts_Pairs01	Endosymbionts_Pairs01
Endosymbionts_Pairs02	Endosymbionts_Pairs02
Endosymbionts_Pairs03	Endosymbionts_Pairs03
Endosymbionts_Sets	Endosymbionts_Sets
Endosymbionts_Synteny	Endosymbionts_Synteny
EstimateRearrangementScenarios	EstimRearrScen
EstimRearrScen	EstimRearrScen
ExampleStreptomycesData	ExampleStreptomycesData
ExtractBy	ExtractBy
FindSets	FindSets
GainLoss.ProtWeaver	ProtWeaver-PAPreds
Generic	Generic
gffToDataFrame	gffToDataFrame
Hamming.ProtWeaver	ProtWeaver-PAPreds
Jaccard.ProtWeaver	ProtWeaver-PAPreds
JRFDist	PhyloDistance-JRF
KFDist	PhyloDistance-KF
LinkedPairs-class	LinkedPairs-class
MirrorTree.ProtWeaver	ProtWeaver-DMPreds
MoransI	MoransI
MutualInformation.ProtWeaver	ProtWeaver-PAPreds
NucleotideOverlap	NucleotideOverlap
PairSummaries	PairSummaries
PhyloDistance	PhyloDistance
PhyloDistance-CI	PhyloDistance-CI
PhyloDistance-JRF	PhyloDistance-JRF
PhyloDistance-KF	PhyloDistance-KF
PhyloDistance-RF	PhyloDistance-RF
plot.ProtWeb	plot.ProtWeb
predict.ProtWeaver	predict.ProtWeaver
print.LinkedPairs	LinkedPairs-class
print.simMat	simMat
ProfDCA.ProtWeaver	ProtWeaver-PAPreds
ProtWeaver	ProtWeaver
ProtWeaver-class	ProtWeaver
ProtWeaver-ColocPreds	ProtWeaver-ColocPreds
ProtWeaver-DMPreds	ProtWeaver-DMPreds
ProtWeaver-PAPreds	ProtWeaver-PAPreds
ProtWeaver-ResiduePreds	ProtWeaver-ResiduePreds
ProtWeaver-utils	ProtWeaver
ProtWeb	ProtWeb
ResidueMI.ProtWeaver	ProtWeaver-ResiduePreds
RFDist	PhyloDistance-RF
SelectByK	SelectByK
SequenceSimilarity	SequenceSimilarity
simMat	simMat
simMat-class	simMat
SpeciesTree	ProtWeaver
SpeciesTree.ProtWeaver	ProtWeaver
SubSetPairs	SubSetPairs
SuperTree	SuperTree
SuperTreeEx	SuperTreeEx
[.LinkedPairs	LinkedPairs-class
