addMSA                  Prepare data for sitePath analysis
extractTips             Extract info for fixation of a single site
findSites               Finding sites with variation
h3n2_align              Multiple sequence alignment of H3N2's HA
                        protein
h3n2_align_reduced      Truncated data for runnable example
h3n2_tree               Phylogenetic tree of H3N2's HA protein
h3n2_tree_reduced       Truncated data for runnable example
plot.lineagePath        Visualize phylogenetic lineages
plot.sitePath           Plot the fixation mutation
plotSingleSite          Color the tree by a single site
pre-assessment          Things can be done before the analysis
setSiteNumbering        Set site numbering to the reference sequence
treemer                 Topology-dependent tree trimming
zikv_align              Multiple sequence alignment of Zika virus
                        polyprotein
zikv_align_reduced      Truncated data for runnable example
zikv_tree               Phylogenetic tree of Zika virus polyprotein
zikv_tree_reduced       Truncated data for runnable example
