addMSA	addMSA
extractSite	extractTips
extractSite.fixationSites	extractTips
extractSite.multiFixationSites	extractTips
extractTips	extractTips
extractTips.fixationSites	extractTips
extractTips.multiFixationSites	extractTips
extractTips.sitePath	extractTips
findSites	findSites
fixationSites	findSites
fixationSites.lineagePath	findSites
groupTips	treemer
h3n2_align	h3n2_align
h3n2_align_reduced	h3n2_align_reduced
h3n2_tree	h3n2_tree
h3n2_tree_reduced	h3n2_tree_reduced
lineagePath	treemer
multiFixationSites	findSites
multiFixationSites.lineagePath	findSites
plot.lineagePath	plot.lineagePath
plot.sitePath	plot.sitePath
plotSingleSite	plotSingleSite
plotSingleSite.fixationSites	plotSingleSite
plotSingleSite.lineagePath	plotSingleSite
plotSingleSite.multiFixationSites	plotSingleSite
pre-assessment	pre-assessment
setSiteNumbering	setSiteNumbering
setSiteNumbering.lineagePath	setSiteNumbering
setSiteNumbering.phylo	setSiteNumbering
similarityMatrix	pre-assessment
sneakPeek	pre-assessment
SNPsites	findSites
treemer	treemer
zikv_align	zikv_align
zikv_align_reduced	zikv_align_reduced
zikv_tree	zikv_tree
zikv_tree_reduced	zikv_tree_reduced
