Man pages for wuaipinglab/sitePath
Phylogeny-based sequence clustering with site polymorphism

addMSAAdd matching sequence alignment to the tree
allSitesNameRetrieve position of all the sites results to Data Frame
extractSiteExtract tips for a single site
extractTipsExtract grouped tips for a single site
fixationIndelsFixation indels prediction
fixationPathAccumulation of fixed mutation as a tree
fixationSitesFixation sites prediction
groupTipsThe grouping of tree tips
h3n2_alignMultiple sequence alignment of H3N2's HA protein
h3n2_treePhylogenetic tree of H3N2's HA protein
lineagePathResolving lineage paths using SNP
paraFixSitesThe fixation sites with mutation on parallel lineage
parallelSitesMutation across multiple phylogenetic lineages
plotFixationSitesPlot the result of fixation sites
plotFunctionsVisualize the results
plotMutSitesPlot tree and mutation sites
plotParallelSitesPlot the result of fixation sites
plotSingleSiteColor the tree by a single site
reexportsObjects exported from other packages
sars2_alignMultiple sequence alignment of SARS-CoV-2 genome CDS
sars2_treePhylogenetic tree of SARS-CoV-2 genome CDS
setSiteNumberingSet site numbering to the reference sequence
similarityMatrixSimilarity between sequences
sitePath-deprecatedDeprecated functions in package 'sitePath'
sitesMinEntropyFixation sites prediction
SNPsitesFinding sites with variation
zikv_alignMultiple sequence alignment of Zika virus polyprotein
zikv_treePhylogenetic tree of Zika virus polyprotein
wuaipinglab/sitePath documentation built on Sept. 26, 2022, 10:16 p.m.