addMSA	addMSA
addMSA.phylo	addMSA
addMSA.treedata	addMSA
allSitesName	allSitesName
allSitesName.fixationSites	allSitesName
allSitesName.paraFixSites	allSitesName
allSitesName.parallelSites	allSitesName
allSitesName.sitesMinEntropy	allSitesName
allSitesName.SNPsites	allSitesName
as.data.frame.fixationSites	as.data.frame
as.data.frame.parallelSites	as.data.frame
as.data.frame.SNPsites	as.data.frame
as.phylo	reexports
as.treedata	reexports
extractSite	extractSite
extractSite.fixationSites	extractSite
extractTips	extractTips
extractTips.fixationSites	extractTips
extractTips.lineagePath	extractTips
extractTips.parallelSites	extractTips
extractTips.sitePara	extractTips
extractTips.sitePath	extractTips
extractTips.sitesMinEntropy	extractTips
fixationIndels	fixationIndels
fixationIndels.sitesMinEntropy	fixationIndels
fixationPath	fixationPath
fixationPath.fixationSites	fixationPath
fixationPath.sitesMinEntropy	fixationPath
fixationSites	fixationSites
fixationSites.lineagePath	fixationSites
fixationSites.paraFixSites	fixationSites
fixationSites.sitesMinEntropy	fixationSites
groupTips	groupTips
groupTips.fixationPath	groupTips
groupTips.fixationSites	groupTips
groupTips.lineagePath	groupTips
groupTips.phyMSAmatched	groupTips
groupTips.sitesMinEntropy	groupTips
h3n2_align	h3n2_align
h3n2_align_reduced	h3n2_align
h3n2_tree	h3n2_tree
h3n2_tree_reduced	h3n2_tree
lineagePath	lineagePath
lineagePath.paraFixSites	lineagePath
lineagePath.phylo	lineagePath
lineagePath.phyMSAmatched	lineagePath
lineagePath.sneakPeekedPaths	lineagePath
lineagePath.treedata	lineagePath
multiFixationSites	sitePath-deprecated
paraFixSites	paraFixSites
paraFixSites.lineagePath	paraFixSites
paraFixSites.phylo	paraFixSites
paraFixSites.sitesMinEntropy	paraFixSites
paraFixSites.treedata	paraFixSites
parallelSites	parallelSites
parallelSites.lineagePath	parallelSites
parallelSites.paraFixSites	parallelSites
parallelSites.sitesMinEntropy	parallelSites
phyMSAmatched	addMSA
plot.fixationIndels	plotFunctions
plot.fixationPath	plotFunctions
plot.fixationSites	plotFunctions
plot.lineagePath	plotFunctions
plot.parallelSites	plotFunctions
plot.phyMSAmatched	plotFunctions
plot.sitePath	plotFunctions
plotFixationSites	plotFixationSites
plotFixationSites.fixationSites	plotFixationSites
plotFixationSites.paraFixSites	plotFixationSites
plotMutSites	plotMutSites
plotMutSites.fixationSites	plotMutSites
plotMutSites.lineagePath	plotMutSites
plotMutSites.paraFixSites	plotMutSites
plotMutSites.parallelSites	plotMutSites
plotMutSites.SNPsites	plotMutSites
plotParallelSites	plotParallelSites
plotParallelSites.paraFixSites	plotParallelSites
plotParallelSites.parallelSites	plotParallelSites
plotSingleSite	plotSingleSite
plotSingleSite.fixationSites	plotSingleSite
plotSingleSite.lineagePath	plotSingleSite
plotSingleSite.parallelSites	plotSingleSite
plotSingleSite.sitesMinEntropy	plotSingleSite
read.alignment	reexports
read.tree	reexports
reexports	reexports
sars2_align	sars2_align
sars2_tree	sars2_tree
setSiteNumbering	setSiteNumbering
setSiteNumbering.phyMSAmatched	setSiteNumbering
similarityMatrix	similarityMatrix
sitePath-deprecated	sitePath-deprecated
sitesMinEntropy	sitesMinEntropy
sitesMinEntropy.lineagePath	sitesMinEntropy
sneakPeek	lineagePath
SNPsites	SNPsites
SNPsites.phyMSAmatched	SNPsites
zikv_align	zikv_align
zikv_align_reduced	zikv_align
zikv_tree	zikv_tree
zikv_tree_reduced	zikv_tree
