Phylogenetic pathway–dependent recognition of fixed
substitutions and parallel mutations
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Documentation for package ‘sitePath’ version 1.10.1
Help Pages
| addMSA | Add matching sequence alignment to the tree |
| addMSA.phylo | Add matching sequence alignment to the tree |
| addMSA.treedata | Add matching sequence alignment to the tree |
| allSitesName | Retrieve position of all the sites |
| allSitesName.fixationSites | Retrieve position of all the sites |
| allSitesName.paraFixSites | Retrieve position of all the sites |
| allSitesName.parallelSites | Retrieve position of all the sites |
| allSitesName.SNPsites | Retrieve position of all the sites |
| as.data.frame.fixationSites | Convert results to Data Frame |
| as.data.frame.parallelSites | Convert results to Data Frame |
| as.data.frame.SNPsites | Convert results to Data Frame |
| extractSite | Extract tips for a single site |
| extractSite.fixationSites | Extract tips for a single site |
| extractTips | Extract grouped tips for a single site |
| extractTips.fixationSites | Extract grouped tips for a single site |
| extractTips.lineagePath | Extract grouped tips for a single site |
| extractTips.parallelSites | Extract grouped tips for a single site |
| extractTips.sitePara | Extract grouped tips for a single site |
| extractTips.sitePath | Extract grouped tips for a single site |
| fixationIndels | Fixation indels prediction |
| fixationIndels.sitesMinEntropy | Fixation indels prediction |
| fixationPath | Accumulation of fixed mutation as a tree |
| fixationPath.fixationSites | Accumulation of fixed mutation as a tree |
| fixationPath.sitesMinEntropy | Accumulation of fixed mutation as a tree |
| fixationSites | Fixation sites prediction |
| fixationSites.lineagePath | Fixation sites prediction |
| fixationSites.sitesMinEntropy | Fixation sites prediction |
| groupTips | The grouping of tree tips |
| groupTips.fixationPath | The grouping of tree tips |
| groupTips.fixationSites | The grouping of tree tips |
| groupTips.lineagePath | The grouping of tree tips |
| groupTips.phyMSAmatched | The grouping of tree tips |
| groupTips.sitesMinEntropy | The grouping of tree tips |
| h3n2_align | Multiple sequence alignment of H3N2's HA protein |
| h3n2_align_reduced | Multiple sequence alignment of H3N2's HA protein |
| h3n2_tree | Phylogenetic tree of H3N2's HA protein |
| h3n2_tree_reduced | Phylogenetic tree of H3N2's HA protein |
| lineagePath | Resolving lineage paths using SNP |
| lineagePath.phyMSAmatched | Resolving lineage paths using SNP |
| lineagePath.sneakPeekedPaths | Resolving lineage paths using SNP |
| multiFixationSites | Deprecated functions in package 'sitePath' |
| paraFixSites | The fixation sites with mutation on parallel lineage |
| paraFixSites.lineagePath | The fixation sites with mutation on parallel lineage |
| paraFixSites.phylo | The fixation sites with mutation on parallel lineage |
| paraFixSites.sitesMinEntropy | The fixation sites with mutation on parallel lineage |
| parallelSites | Mutation across multiple phylogenetic lineages |
| parallelSites.lineagePath | Mutation across multiple phylogenetic lineages |
| parallelSites.sitesMinEntropy | Mutation across multiple phylogenetic lineages |
| phyMSAmatched | Add matching sequence alignment to the tree |
| plot.fixationIndels | Visualize the results |
| plot.fixationPath | Visualize the results |
| plot.fixationSites | Visualize the results |
| plot.lineagePath | Visualize the results |
| plot.parallelSites | Visualize the results |
| plot.phyMSAmatched | Visualize the results |
| plot.sitePath | Visualize the results |
| plotFixationSites | Plot the result of fixation sites |
| plotFixationSites.fixationSites | Plot the result of fixation sites |
| plotFixationSites.paraFixSites | Plot the result of fixation sites |
| plotMutSites | Plot tree and mutation sites |
| plotMutSites.fixationSites | Plot tree and mutation sites |
| plotMutSites.lineagePath | Plot tree and mutation sites |
| plotMutSites.paraFixSites | Plot tree and mutation sites |
| plotMutSites.parallelSites | Plot tree and mutation sites |
| plotMutSites.SNPsites | Plot tree and mutation sites |
| plotParallelSites | Plot the result of fixation sites |
| plotParallelSites.paraFixSites | Plot the result of fixation sites |
| plotParallelSites.parallelSites | Plot the result of fixation sites |
| 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.parallelSites | 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 |
| setSiteNumbering.phyMSAmatched | Set site numbering to the reference sequence |
| similarityMatrix | Similarity between sequences |
| sitePath-deprecated | Deprecated functions in package 'sitePath' |
| sitesMinEntropy | Fixation sites prediction |
| sitesMinEntropy.lineagePath | Fixation sites prediction |
| sneakPeek | Resolving lineage paths using SNP |
| SNPsites | Finding sites with variation |
| SNPsites.phyMSAmatched | Finding sites with variation |
| zikv_align | Multiple sequence alignment of Zika virus polyprotein |
| zikv_align_reduced | Multiple sequence alignment of Zika virus polyprotein |
| zikv_tree | Phylogenetic tree of Zika virus polyprotein |
| zikv_tree_reduced | Phylogenetic tree of Zika virus polyprotein |