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
