Files in cromanpa94/phruta
Phylogenetic Reconstruction and Time-dating
.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
.travis.yml
CONTRIBUTING
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/SW.phruta.R
R/acc.retrieve.R
R/acc.table.retrieve.R
R/gene.sampling.retrieve.R
R/getListConstraints.R
R/globals.R
R/init.R
R/sq.add.R
R/sq.aln.R
R/sq.curate.R
R/sq.partitionfinderv1.R
R/sq.retrieve.direct.R
R/sq.retrieve.indirect.R
R/taxonomy.retrieve.R
R/tree.constraint.R
R/tree.dating.R
R/tree.raxml.R
R/tree.roguetaxa.R
README.md
_pkgdown.yml
codecov.yml
codemeta.json
data/SW.phruta.RData
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/Brief_Intro_phruta.html
docs/articles/Brief_Intro_phruta_files/figure-html/unnamed-chunk-13-1.png
docs/articles/Brief_Intro_phruta_files/figure-html/unnamed-chunk-14-1.png
docs/articles/Brief_Intro_phruta_files/header-attrs-2.9/header-attrs.js
docs/articles/EDF.Cur.jpeg
docs/articles/EDF.Raw.jpeg
docs/articles/Exporting_data_phruta.html
docs/articles/Exporting_data_phruta_files/figure-html/unnamed-chunk-13-1.png
docs/articles/Exporting_data_phruta_files/figure-html/unnamed-chunk-14-1.png
docs/articles/Exporting_data_phruta_files/figure-html/unnamed-chunk-16-1.png
docs/articles/Fig1.png
docs/articles/Fig2.png
docs/articles/Future_phruta.html
docs/articles/IngroupOutgroup.jpg
docs/articles/PTG.Cur.jpeg
docs/articles/PTG.Raw.jpeg
docs/articles/Phruta_advanced.html
docs/articles/Phruta_advanced_files/header-attrs-2.9/header-attrs.js
docs/articles/Phylogenetics_phruta.html
docs/articles/UF.Cur.jpeg
docs/articles/UF.Raw.jpeg
docs/articles/UFE.Cur.jpeg
docs/articles/UFE.Raw.jpeg
docs/articles/Using_phruta.html
docs/articles/Using_phruta_files/figure-html/unnamed-chunk-13-1.png
docs/articles/Using_phruta_files/figure-html/unnamed-chunk-14-1.png
docs/articles/Using_phruta_files/figure-html/unnamed-chunk-16-1.png
docs/articles/byclade.jpg
docs/articles/index.html
docs/articles/logo.png
docs/articles/package_acknowledgements.html
docs/articles/phruta.html
docs/articles/phruta_targetgenes.html
docs/articles/phruta_targetgenes_files/figure-html/unnamed-chunk-10-1.png
docs/articles/phruta_targetgenes_files/figure-html/unnamed-chunk-8-1.png
docs/articles/phruta_vignette.html
docs/articles/phruta_vignette_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/phruta_vignette_files/header-attrs-2.9/header-attrs.js
docs/articles/tree.png
docs/articles/usando_phruta.html
docs/articles/usando_phruta_files/figure-html/unnamed-chunk-14-1.png
docs/articles/usando_phruta_files/figure-html/unnamed-chunk-16-1.png
docs/articles/what_is_phruta.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/SW.phruta.html
docs/reference/TTOL.html
docs/reference/acc.retrieve.html
docs/reference/acc.table.retrieve.html
docs/reference/figures/logo.png
docs/reference/gene.sampling.retrieve.html
docs/reference/getListConstraints.html
docs/reference/index.html
docs/reference/sq.add.html
docs/reference/sq.aln.html
docs/reference/sq.curate.html
docs/reference/sq.partitionfinderv1.html
docs/reference/sq.retrieve.direct.html
docs/reference/sq.retrieve.html
docs/reference/sq.retrieve.indirect.html
docs/reference/taxonomy.retrieve.html
docs/reference/tree.constraint.html
docs/reference/tree.dating.html
docs/reference/tree.raxml.html
docs/reference/tree.roguetaxa.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/WORDLIST
man/SW.phruta.Rd
man/acc.retrieve.Rd
man/acc.table.retrieve.Rd
man/figures/logo.png
man/gene.sampling.retrieve.Rd
man/getListConstraints.Rd
man/sq.add.Rd
man/sq.aln.Rd
man/sq.curate.Rd
man/sq.partitionfinderv1.Rd
man/sq.retrieve.direct.Rd
man/sq.retrieve.indirect.Rd
man/taxonomy.retrieve.Rd
man/tree.constraint.Rd
man/tree.dating.Rd
man/tree.raxml.Rd
man/tree.roguetaxa.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
tests/testthat.R
tests/testthat/helper-testMode.R
tests/testthat/test_SampleData.R
tests/testthat/test_pipeline.direct.R
tests/testthat/test_pipeline.indirect.R
tests/testthat/test_pipeline.indirect.noDownload.R
tests/testthat/test_sq.add.R
tests/testthat/test_sq.aln.R
tests/testthat/test_sq.curate.R
tests/testthat/test_sq.retrieve.direct.R
tests/testthat/test_tree.dating.R
tests/testthat/test_tree.raxml.R
vignettes/EDF.Cur.jpeg
vignettes/EDF.Raw.jpeg
vignettes/Exporting_data_phruta.Rmd
vignettes/Exporting_data_phruta.Rmd.orig
vignettes/Future_phruta.Rmd
vignettes/Future_phruta.Rmd.orig
vignettes/IngroupOutgroup.jpg
vignettes/PTG.Cur.jpeg
vignettes/PTG.Raw.jpeg
vignettes/Phruta_advanced.Rmd
vignettes/Phruta_advanced.Rmd.orig
vignettes/Phylogenetics_phruta.Rmd
vignettes/Phylogenetics_phruta.Rmd.orig
vignettes/UF.Cur.jpeg
vignettes/UF.Raw.jpeg
vignettes/UFE.Cur.jpeg
vignettes/UFE.Raw.jpeg
vignettes/Using_phruta.Rmd
vignettes/Using_phruta.Rmd.orig
vignettes/byclade.jpg
vignettes/logo.png
vignettes/package_acknowledgements.Rmd
vignettes/phruta.Rmd
vignettes/phruta.Rmd.orig
vignettes/phruta_targetgenes.Rmd
vignettes/phruta_targetgenes.Rmd.orig
vignettes/precompile.R
vignettes/tree.png
vignettes/usando_phruta.Rmd
vignettes/usando_phruta.Rmd.orig
