allSitesName            Retrieve position of all the sites
as.data.frame.fixationSites
                        Convert results to Data Frame
extractSite             Extract tips for a single site
extractTips             Extract grouped tips for a single site
fixationPath            Accumulation of fixed mutation as a tree
fixationSites           Fixation sites prediction
groupTips               The grouping of tree tips
h3n2_align              Multiple sequence alignment of H3N2's HA
                        protein
h3n2_tree               Phylogenetic tree of H3N2's HA protein
lineagePath             Resolving lineage paths using SNP
parallelSites           Mutation across multiple phylogenetic lineages
phyMSAmatched           Add matching sequence alignment to the tree
plot.phyMSAmatched      Visualize the results
plotMutSites            Plot tree and mutation 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     Deprecated functions in package 'sitePath'
sitesMinEntropy         Fixation sites prediction
SNPsites                Finding sites with variation
zikv_align              Multiple sequence alignment of Zika virus
                        polyprotein
zikv_tree               Phylogenetic tree of Zika virus polyprotein
