# Phylogeny-based sequence clustering with site polymorphism

## Documentation for package ‘sitePath’ version 1.14.0

- 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