Introduction | Clustering phylogenetic terminals | Import tree file | Import sequence alignment file | Clustering using site polymorphism | Identifying phylogenetic pathways | The impact of threshold on resolving lineages | Choose a threshold | Finding fixed and parallel mutations | Entropy minimization | Fixation mutations | Parallel mutations | Miscellaneous | Inspect one site | SNP sites | Session info
Package: sitePath 1.29.0
Chengyang Ji
sitePath: Phylogeny-based sequence clustering with site polymorphism
Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.
Authors:
sitePath_1.29.0.tar.gz
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sitePath_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
sitePath/json (API)
| # Install 'sitePath' in R: |
| install.packages('sitePath', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wuaipinglab/sitepath/issues
Pkgdown/docs site:https://wuaipinglab.github.io
Datasets:
- 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
- sars2_align - Multiple sequence alignment of SARS-CoV-2 genome CDS
- sars2_tree - Phylogenetic tree of SARS-CoV-2 genome CDS
- 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
On BioConductor:sitePath-1.29.0(bioc 3.24)sitePath-1.28.0(bioc 3.23)
alignmentmultiplesequencealignmentphylogeneticssnpsoftwaremutationcpp
Last updated from:0b270a1503. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 200 | ||
| linux-devel-arm64 | NOTE | 453 | ||
| linux-devel-x86_64 | NOTE | 546 | ||
| source / vignettes | OK | 269 | ||
| linux-release-arm64 | NOTE | 465 | ||
| linux-release-x86_64 | NOTE | 496 | ||
| macos-release-arm64 | NOTE | 326 | ||
| macos-release-x86_64 | NOTE | 670 | ||
| macos-oldrel-arm64 | NOTE | 272 | ||
| macos-oldrel-x86_64 | NOTE | 558 | ||
| windows-devel | NOTE | 496 | ||
| windows-release | NOTE | 488 | ||
| windows-oldrel | NOTE | 490 | ||
| wasm-release | OK | 191 |
Exports:addMSAallSitesNameas.phyloas.treedataextractSiteextractTipsfixationIndelsfixationPathfixationSitesgroupTipslineagePathmultiFixationSitesparaFixSitesparallelSitesplotFixationSitesplotMutSitesplotParallelSitesplotSingleSiteread.alignmentread.treesetSiteNumberingsimilarityMatrixsitesMinEntropysneakPeekSNPsites
Dependencies:ade4apeaplotbase64encbslibcachemclicpp11digestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggfunggiraphggplot2ggplotifyggrepelggtreegluegridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelazyevallifecyclemagrittrMASSmemoisemimenlmepatchworkpillarpixmappkgconfigpurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownS7sassscalessegmentedseqinrspstringistringrsystemfontstibbletidyrtidyselecttidytreetinytextreeioutf8vctrsviridisLitewithrxfunyamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Retrieve position of all the sites | allSitesName allSitesName.fixationSites allSitesName.paraFixSites allSitesName.parallelSites allSitesName.sitesMinEntropy allSitesName.SNPsites |
| Convert results to Data Frame | as.data.frame.fixationSites as.data.frame.parallelSites as.data.frame.SNPsites |
| Extract tips for a single site | extractSite extractSite.fixationSites |
| Extract grouped tips for a single site | extractTips extractTips.fixationSites extractTips.lineagePath extractTips.parallelSites extractTips.sitePara extractTips.sitePath extractTips.sitesMinEntropy |
| Fixation indels prediction | fixationIndels fixationIndels.sitesMinEntropy |
| Accumulation of fixed mutation as a tree | fixationPath fixationPath.fixationSites fixationPath.sitesMinEntropy |
| Fixation sites prediction | fixationSites fixationSites.lineagePath fixationSites.paraFixSites fixationSites.sitesMinEntropy |
| The grouping of tree tips | groupTips groupTips.fixationPath groupTips.fixationSites groupTips.lineagePath groupTips.phyMSAmatched groupTips.sitesMinEntropy |
| Multiple sequence alignment of H3N2's HA protein | h3n2_align h3n2_align_reduced |
| Phylogenetic tree of H3N2's HA protein | h3n2_tree h3n2_tree_reduced |
| Resolving lineage paths using SNP | lineagePath lineagePath.paraFixSites lineagePath.phylo lineagePath.phyMSAmatched lineagePath.sneakPeekedPaths lineagePath.treedata sneakPeek |
| The fixation sites with mutation on parallel lineage | paraFixSites paraFixSites.lineagePath paraFixSites.phylo paraFixSites.sitesMinEntropy paraFixSites.treedata |
| Mutation across multiple phylogenetic lineages | parallelSites parallelSites.lineagePath parallelSites.paraFixSites parallelSites.sitesMinEntropy |
| Add matching sequence alignment to the tree | addMSA addMSA.phylo addMSA.treedata phyMSAmatched |
| Visualize the results | plot.fixationIndels plot.fixationPath plot.fixationSites plot.lineagePath plot.parallelSites plot.phyMSAmatched plot.sitePath |
| Plot the result of fixation sites | plotFixationSites plotFixationSites.fixationSites plotFixationSites.paraFixSites |
| Plot tree and mutation sites | plotMutSites plotMutSites.fixationSites plotMutSites.lineagePath plotMutSites.paraFixSites plotMutSites.parallelSites plotMutSites.SNPsites |
| Plot the result of fixation sites | plotParallelSites plotParallelSites.paraFixSites plotParallelSites.parallelSites |
| Color the tree by a single site | plotSingleSite plotSingleSite.fixationSites plotSingleSite.lineagePath plotSingleSite.parallelSites plotSingleSite.sitesMinEntropy |
| Multiple sequence alignment of SARS-CoV-2 genome CDS | sars2_align |
| Phylogenetic tree of SARS-CoV-2 genome CDS | sars2_tree |
| Set site numbering to the reference sequence | setSiteNumbering setSiteNumbering.phyMSAmatched |
| Similarity between sequences | similarityMatrix |
| Deprecated functions in package 'sitePath' | multiFixationSites sitePath-deprecated |
| Fixation sites prediction | sitesMinEntropy sitesMinEntropy.lineagePath |
| Finding sites with variation | SNPsites SNPsites.phyMSAmatched |
| Multiple sequence alignment of Zika virus polyprotein | zikv_align zikv_align_reduced |
| Phylogenetic tree of Zika virus polyprotein | zikv_tree zikv_tree_reduced |
