Ancestral.EvoWeaver	EvoWeaver-SLPreds
as.data.frame.simMat	simMat
as.matrix.simMat	simMat
as.simMat	simMat
as.simMat.matrix	simMat
as.simMat.vector	simMat
Behdenna.EvoWeaver	EvoWeaver-PPPreds
BlastSeqs	BlastSeqs
BlockExpansion	BlockExpansion
BlockReconciliation	BlockReconciliation
BuiltInEnsembles	BuiltInEnsembles
CIDist	PhyloDistance-CI
CIDist_NullDist	CIDist_NullDist
Coloc.EvoWeaver	EvoWeaver-GOPreds
ColocMoran.EvoWeaver	EvoWeaver-GOPreds
ContextTree.EvoWeaver	EvoWeaver-PSPreds
CorrGL.EvoWeaver	EvoWeaver-PPPreds
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
EvoWeaver	EvoWeaver
EvoWeaver-class	EvoWeaver
EvoWeaver-GOPreds	EvoWeaver-GOPreds
EvoWeaver-PPPreds	EvoWeaver-PPPreds
EvoWeaver-PSPreds	EvoWeaver-PSPreds
EvoWeaver-SLPreds	EvoWeaver-SLPreds
EvoWeaver-utils	EvoWeaver
EvoWeb	EvoWeb
ExampleStreptomycesData	ExampleStreptomycesData
ExtractBy	ExtractBy
FastQFromSRR	FastQFromSRR
FindSets	FindSets
FitchParsimony	FitchParsimony
GainLoss.EvoWeaver	EvoWeaver-PPPreds
Generic	Generic
gffToDataFrame	gffToDataFrame
Hamming.EvoWeaver	EvoWeaver-PPPreds
Jaccard.EvoWeaver	EvoWeaver-PPPreds
JRFDist	PhyloDistance-JRF
KFDist	PhyloDistance-KF
LinkedPairs-class	LinkedPairs-class
MakeBlastDb	MakeBlastDb
MirrorTree.EvoWeaver	EvoWeaver-PSPreds
MoransI	MoransI
MutualInformation.EvoWeaver	EvoWeaver-PPPreds
NucleotideOverlap	NucleotideOverlap
NVDT.EvoWeaver	EvoWeaver-SLPreds
PairSummaries	PairSummaries
PhyloDistance	PhyloDistance
PhyloDistance-CI	PhyloDistance-CI
PhyloDistance-JRF	PhyloDistance-JRF
PhyloDistance-KF	PhyloDistance-KF
PhyloDistance-RF	PhyloDistance-RF
plot.EvoWeb	plot.EvoWeb
predict.EvoWeaver	predict.EvoWeaver
print.LinkedPairs	LinkedPairs-class
print.simMat	simMat
ProfDCA.EvoWeaver	EvoWeaver-PPPreds
ResidueMI.EvoWeaver	EvoWeaver-SLPreds
RFDist	PhyloDistance-RF
SelectByK	SelectByK
SequenceSimilarity	SequenceSimilarity
simMat	simMat
simMat-class	simMat
SpeciesTree	EvoWeaver
SpeciesTree.EvoWeaver	EvoWeaver
subset.dendrogram	subset-dendrogram
SubSetPairs	SubSetPairs
SuperTree	SuperTree
SuperTreeEx	SuperTreeEx
TranscripMI.EvoWeaver	EvoWeaver-GOPreds
TreeDistance.EvoWeaver	EvoWeaver-PSPreds
[.LinkedPairs	LinkedPairs-class
