Phylogeny-based sequence clustering with site polymorphism

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Documentation for package ‘sitePath’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addMSA	Add matching sequence alignment to the tree
addMSA.phylo	Add matching sequence alignment to the tree
addMSA.treedata	Add matching sequence alignment to the tree
allSitesName	Retrieve position of all the sites
allSitesName.fixationSites	Retrieve position of all the sites
allSitesName.paraFixSites	Retrieve position of all the sites
allSitesName.parallelSites	Retrieve position of all the sites
allSitesName.sitesMinEntropy	Retrieve position of all the sites
allSitesName.SNPsites	Retrieve position of all the sites
as.data.frame.fixationSites	Convert results to Data Frame
as.data.frame.parallelSites	Convert results to Data Frame
as.data.frame.SNPsites	Convert results to Data Frame
extractSite	Extract tips for a single site
extractSite.fixationSites	Extract tips for a single site
extractTips	Extract grouped tips for a single site
extractTips.fixationSites	Extract grouped tips for a single site
extractTips.lineagePath	Extract grouped tips for a single site
extractTips.parallelSites	Extract grouped tips for a single site
extractTips.sitePara	Extract grouped tips for a single site
extractTips.sitePath	Extract grouped tips for a single site
extractTips.sitesMinEntropy	Extract grouped tips for a single site
fixationIndels	Fixation indels prediction
fixationIndels.sitesMinEntropy	Fixation indels prediction
fixationPath	Accumulation of fixed mutation as a tree
fixationPath.fixationSites	Accumulation of fixed mutation as a tree
fixationPath.sitesMinEntropy	Accumulation of fixed mutation as a tree
fixationSites	Fixation sites prediction
fixationSites.lineagePath	Fixation sites prediction
fixationSites.paraFixSites	Fixation sites prediction
fixationSites.sitesMinEntropy	Fixation sites prediction
groupTips	The grouping of tree tips
groupTips.fixationPath	The grouping of tree tips
groupTips.fixationSites	The grouping of tree tips
groupTips.lineagePath	The grouping of tree tips
groupTips.phyMSAmatched	The grouping of tree tips
groupTips.sitesMinEntropy	The grouping of tree tips
h3n2_align	Multiple sequence alignment of H3N2's HA protein
h3n2_align_reduced	Multiple sequence alignment of H3N2's HA protein
h3n2_tree	Phylogenetic tree of H3N2's HA protein
h3n2_tree_reduced	Phylogenetic tree of H3N2's HA protein
lineagePath	Resolving lineage paths using SNP
lineagePath.paraFixSites	Resolving lineage paths using SNP
lineagePath.phylo	Resolving lineage paths using SNP
lineagePath.phyMSAmatched	Resolving lineage paths using SNP
lineagePath.sneakPeekedPaths	Resolving lineage paths using SNP
lineagePath.treedata	Resolving lineage paths using SNP
multiFixationSites	Deprecated functions in package 'sitePath'
paraFixSites	The fixation sites with mutation on parallel lineage
paraFixSites.lineagePath	The fixation sites with mutation on parallel lineage
paraFixSites.phylo	The fixation sites with mutation on parallel lineage
paraFixSites.sitesMinEntropy	The fixation sites with mutation on parallel lineage
paraFixSites.treedata	The fixation sites with mutation on parallel lineage
parallelSites	Mutation across multiple phylogenetic lineages
parallelSites.lineagePath	Mutation across multiple phylogenetic lineages
parallelSites.paraFixSites	Mutation across multiple phylogenetic lineages
parallelSites.sitesMinEntropy	Mutation across multiple phylogenetic lineages
phyMSAmatched	Add matching sequence alignment to the tree
plot.fixationIndels	Visualize the results
plot.fixationPath	Visualize the results
plot.fixationSites	Visualize the results
plot.lineagePath	Visualize the results
plot.parallelSites	Visualize the results
plot.phyMSAmatched	Visualize the results
plot.sitePath	Visualize the results
plotFixationSites	Plot the result of fixation sites
plotFixationSites.fixationSites	Plot the result of fixation sites
plotFixationSites.paraFixSites	Plot the result of fixation sites
plotMutSites	Plot tree and mutation sites
plotMutSites.fixationSites	Plot tree and mutation sites
plotMutSites.lineagePath	Plot tree and mutation sites
plotMutSites.paraFixSites	Plot tree and mutation sites
plotMutSites.parallelSites	Plot tree and mutation sites
plotMutSites.SNPsites	Plot tree and mutation sites
plotParallelSites	Plot the result of fixation sites
plotParallelSites.paraFixSites	Plot the result of fixation sites
plotParallelSites.parallelSites	Plot the result of fixation sites
plotSingleSite	Color the tree by a single site
plotSingleSite.fixationSites	Color the tree by a single site
plotSingleSite.lineagePath	Color the tree by a single site
plotSingleSite.parallelSites	Color the tree by a single site
plotSingleSite.sitesMinEntropy	Color the tree by a single site
sars2_align	Multiple sequence alignment of SARS-CoV-2 genome CDS
sars2_tree	Phylogenetic tree of SARS-CoV-2 genome CDS
setSiteNumbering	Set site numbering to the reference sequence
setSiteNumbering.phyMSAmatched	Set site numbering to the reference sequence
similarityMatrix	Similarity between sequences
sitePath-deprecated	Deprecated functions in package 'sitePath'
sitesMinEntropy	Fixation sites prediction
sitesMinEntropy.lineagePath	Fixation sites prediction
sneakPeek	Resolving lineage paths using SNP
SNPsites	Finding sites with variation
SNPsites.phyMSAmatched	Finding sites with variation
zikv_align	Multiple sequence alignment of Zika virus polyprotein
zikv_align_reduced	Multiple sequence alignment of Zika virus polyprotein
zikv_tree	Phylogenetic tree of Zika virus polyprotein
zikv_tree_reduced	Phylogenetic tree of Zika virus polyprotein