Man pages for Takkoona/sitePath
Phylogeny-based sequence clustering with site polymorphism
| addMSA | Add matching sequence alignment to the tree |
| allSitesName | Retrieve position of all the sites |
| as.data.frame | Convert results to Data Frame |
| extractSite | Extract tips for a single site |
| extractTips | Extract grouped tips for a single site |
| fixationIndels | Fixation indels prediction |
| 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 |
| paraFixSites | The fixation sites with mutation on parallel lineage |
| parallelSites | Mutation across multiple phylogenetic lineages |
| plotFixationSites | Plot the result of fixation sites |
| plotFunctions | Visualize the results |
| plotMutSites | Plot tree and mutation sites |
| plotParallelSites | Plot the result of fixation sites |
| plotSingleSite | Color the tree by a single site |
| reexports | Objects exported from other packages |
| 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 |
