Function reference • sitePath

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

Reference

All functions