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| addMSA | Prepare data for sitePath analysis |
| extractSite | Extract info for fixation of a single site |
| extractSite.fixationSites | Extract info for fixation of a single site |
| extractSite.multiFixationSites | Extract info for fixation of a single site |
| extractTips | Extract info for fixation of a single site |
| extractTips.fixationSites | Extract info for fixation of a single site |
| extractTips.multiFixationSites | Extract info for fixation of a single site |
| extractTips.sitePath | Extract info for fixation of 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 |
| plot.sitePath | Plot the fixation mutation |
| 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 |
| setSiteNumbering | Set site numbering to the reference sequence |
| setSiteNumbering.lineagePath | Set site numbering to the reference sequence |
| setSiteNumbering.phylo | Set site numbering to the reference sequence |
| 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 |