Files in Takkoona/sitePath

Phylogeny-based sequence clustering with site polymorphism

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/check-bioc.yml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/RcppExports.R R/SNPsites.R R/addMSA.R R/allSitesName.R R/as.data.frame.R R/extractSite.R R/extractTips.R R/fixationIndels.R R/fixationPath.R R/fixationSites.R R/groupTips.R R/lineagePath.R R/paraFixSites.R R/parallelSites.R R/plotFixationSites.R R/plotFunctions.R R/plotMutSites.R R/plotParallelSites.R R/plotSingleSite.R R/printFunctions.R R/reexports.R R/siteNumbering.R R/sitePath-deprecated.R R/sitesMinEntropy.R R/staticData.R README.Rmd README.md

data/h3n2_align.rda

data/h3n2_align_reduced.rda

data/h3n2_tree.rda

data/h3n2_tree_reduced.rda

data/sars2_align.rda

data/sars2_tree.rda

data/zikv_align.rda

data/zikv_align_reduced.rda

data/zikv_tree.rda

data/zikv_tree_reduced.rda

inst/extdata/WNV.newick

inst/extdata/ZIKV.fasta

inst/extdata/ZIKV.newick

man/SNPsites.Rd man/addMSA.Rd man/allSitesName.Rd man/as.data.frame.Rd man/extractSite.Rd man/extractTips.Rd

man/figures/example-1.png

man/figures/example-2.png

man/figures/plot_fixSites-1.png

man/figures/plot_fixSites-2.png

man/figures/unnamed-chunk-1-1.png

man/figures/unnamed-chunk-1-2.png

man/fixationIndels.Rd man/fixationPath.Rd man/fixationSites.Rd man/groupTips.Rd man/h3n2_align.Rd man/h3n2_tree.Rd man/lineagePath.Rd man/paraFixSites.Rd man/parallelSites.Rd man/plotFixationSites.Rd man/plotFunctions.Rd man/plotMutSites.Rd man/plotParallelSites.Rd man/plotSingleSite.Rd man/reexports.Rd man/sars2_align.Rd man/sars2_tree.Rd man/setSiteNumbering.Rd man/similarityMatrix.Rd man/sitePath-deprecated.Rd man/sitesMinEntropy.Rd man/zikv_align.Rd man/zikv_tree.Rd

src/.gitignore

src/RcppExports.cpp

src/lumpyCluster.cpp

src/lumpyCluster.h

src/minEntropy.cpp

src/minEntropy.h

src/searchNode.cpp

src/searchTree.cpp

src/treemer.cpp

src/treemer.h

src/util.cpp

tests/testthat.R tests/testthat/test-SNPsites.R tests/testthat/test-addMSA.R tests/testthat/test-allSitesName.R tests/testthat/test-as.data.frame.R tests/testthat/test-fixationPath.R tests/testthat/test-fixationSites.R tests/testthat/test-groupTips.R tests/testthat/test-lineagePath.R tests/testthat/test-multiprocessing.R tests/testthat/test-paraFixSites.R tests/testthat/test-parallelSites.R tests/testthat/test-plotFunctions.R tests/testthat/test-plotSingleSite.R tests/testthat/test-printFunctions.R tests/testthat/test-reexports.R tests/testthat/test-similarityMatrix.R tests/testthat/test-siteNumbering.R tests/testthat/test-sitesMinEntropy.R vignettes/sitePath.Rmd

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.