AAHitScoping	AAHitScoping
Ancestral.EvoWeaver	EvoWeaver-SLPreds
ApproximateBackground	ApproximateBackground
as.data.frame.simMat	simMat
as.dendrogram.DecisionTree	DecisionTree-class
as.matrix.simMat	simMat
as.simMat	simMat
as.simMat.matrix	simMat
as.simMat.vector	simMat
Behdenna.EvoWeaver	EvoWeaver-PPPreds
BlastSeqs	BlastSeqs
BlockByRank	BlockByRank
BlockExpansion	BlockExpansion
BlockReconciliation	BlockReconciliation
BuiltInEnsembles	BuiltInEnsembles
CheckAgainstReport	CheckAgainstReport
CIDist	PhyloDistance-CI
CIDist_NullDist	CIDist_NullDist
ClusterByK	ClusterByK
CompetePairs	CompetePairs
CorrGL.EvoWeaver	EvoWeaver-PPPreds
DecisionTree-class	DecisionTree-class
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
EstimateExoLabel	EstimateExoLabel
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
ExoLabel	ExoLabel
ExpandDiagonal	ExpandDiagonal
ExtantJaccard.EvoWeaver	EvoWeaver-PPPreds
ExtractBy	ExtractBy
FastQFromSRR	FastQFromSRR
FindSets	FindSets
FitchParsimony	FitchParsimony
GeneDistance.EvoWeaver	EvoWeaver-GOPreds
Generic	Generic
GeneVector.EvoWeaver	EvoWeaver-SLPreds
gffToDataFrame	gffToDataFrame
GLDistance.EvoWeaver	EvoWeaver-PPPreds
GLMI.EvoWeaver	EvoWeaver-PPPreds
Hamming.EvoWeaver	EvoWeaver-PPPreds
HitConsensus	HitConsensus
JRFDist	PhyloDistance-JRF
KFDist	PhyloDistance-KF
LinkedPairs-class	LinkedPairs-class
MakeBlastDb	MakeBlastDb
MoranI	MoransI
MoransI.EvoWeaver	EvoWeaver-GOPreds
NormVec	NormVec
NucleotideOverlap	NucleotideOverlap
OneSite	OneSite
OrientationMI.EvoWeaver	EvoWeaver-GOPreds
PairSummaries	PairSummaries
PAJaccard.EvoWeaver	EvoWeaver-PPPreds
PAOverlap.EvoWeaver	EvoWeaver-PPPreds
PhyloDistance	PhyloDistance
PhyloDistance-CI	PhyloDistance-CI
PhyloDistance-JRF	PhyloDistance-JRF
PhyloDistance-KF	PhyloDistance-KF
PhyloDistance-RF	PhyloDistance-RF
plot.DecisionTree	DecisionTree-class
plot.EvoWeb	plot.EvoWeb
predict.EvoWeaver	predict.EvoWeaver
predict.RandForest	RandForest
PrepareSeqs	PrepareSeqs
print.LinkedPairs	LinkedPairs-class
print.simMat	simMat
ProfDCA.EvoWeaver	EvoWeaver-PPPreds
RandForest	RandForest
RandForest.fit	RandForest
RejectionBy	RejectionBy
RFDist	PhyloDistance-RF
RPContextTree.EvoWeaver	EvoWeaver-PSPreds
RPMirrorTree.EvoWeaver	EvoWeaver-PSPreds
SelectByK	SelectByK
SequenceInfo.EvoWeaver	EvoWeaver-SLPreds
SequenceSimilarity	SequenceSimilarity
simMat	simMat
simMat-class	simMat
SpeciesTree	EvoWeaver
SpeciesTree.EvoWeaver	EvoWeaver
subset.dendrogram	subset-dendrogram
SubSetPairs	SubSetPairs
SummarizePairs	SummarizePairs
SuperTree	SuperTree
SuperTreeEx	SuperTreeEx
TreeDistance.EvoWeaver	EvoWeaver-PSPreds
WithinSetCompetition	WithinSetCompetition
[.LinkedPairs	LinkedPairs-class
