addMSA | Prepare data for sitePath analysis |
extractTips | Extract sitePath for a single site |
extractTips.fixationSites | Extract sitePath for a single site |
extractTips.multiFixationSites | Extract sitePath for a single site |
findSites | Finding sites with variation |
fixationSites | Finding sites with variation |
fixationSites.lineagePath | Finding sites with variation |
groupTips | Topology-dependent tree trimming |
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 |
lineagePath | Topology-dependent tree trimming |
multiFixationSites | Finding sites with variation |
multiFixationSites.lineagePath | Finding sites with variation |
plot.lineagePath | Visualize phylogenetic lineages |
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.multiFixationSites | Color the tree by a single site |
pre-assessment | Things can be done before the analysis |
similarityMatrix | Things can be done before the analysis |
sneakPeek | Things can be done before the analysis |
SNPsites | Finding sites with variation |
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 |