Package: phruta 0.1.3

Cristian Roman Palacios

phruta: Phylogenetic Reconstruction and Time-dating

The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.

Authors:Cristian Roman Palacios [aut, cre], Anna Krystalli [rev], Rayna Harris [rev], Frederick Boehm [rev]

phruta_0.1.3.tar.gz
phruta_0.1.3.zip(r-4.7)phruta_0.1.3.zip(r-4.6)phruta_0.1.3.zip(r-4.5)
phruta_0.1.3.tgz(r-4.6-any)phruta_0.1.3.tgz(r-4.5-any)
phruta_0.1.3.tar.gz(r-4.7-any)phruta_0.1.3.tar.gz(r-4.6-any)
phruta_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phruta/json (API)

# Install 'phruta' in R:
install.packages('phruta', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #458

Bug tracker:https://github.com/ropensci/phruta/issues

Pkgdown/docs site:https://docs.ropensci.org

On CRAN:

Conda:

5.21 score 9 stars 20 scripts 13 exports 147 dependencies

Last updated from:6a18ef79a3 (on main). Checks:6 ERROR, 3 OK, 1 NOTE. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR535
pkgdown docsOK442
source / vignettesOK292
linux-release-x86_64ERROR542
macos-release-arm64NOTE567
macos-oldrel-arm64ERROR617
windows-develERROR504
windows-releaseERROR555
windows-oldrelERROR461
wasm-releaseOK227

Exports:acc.table.retrievegene.sampling.retrievegetListConstraintssq.addsq.alnsq.curatesq.partitionfinderv1sq.retrieve.directsq.retrieve.indirecttree.constrainttree.datingtree.raxmltree.roguetaxa

Dependencies:apclusterapeaskpassbase64encBiocGenericsBiostringsbitbit64bslibcachemclasscliclusterGenerationcodacodetoolscolorspacecombinatcommonmarkcpp11crayoncrulcurldata.tableDBIDECIPHERDEoptimdeSolvedigestdoParalleldoSNOWdplyre1071expmfarverfastmapfastmatchfontawesomeforeachfsgeigergenericsggplot2gluegtablehmshtmltoolshttpcodehttpuvhttrigraphipsIRangesisobanditeratorsjquerylibjsonlitekebabskernlablabelinglaterlatticelazyevalLiblineaRlifecyclemagrittrmapsMASSMatrixmatrixStatsmclustmemoisemimemnormtmsaMultipleAlignmentmvtnormnatservncbitnlmenumDerivoaiodseqopenssloptimParallelotelpbapplyphangornphytoolspillarpkgconfigPlotToolsplyrprettyunitsprogresspromisesproxyquadprogR6rappdirsrbibutilsRColorBrewerRcppRdpackrentrezreutilsrgbifritisrlangrnclRoguerotlrredlistS4VectorsS7sassscalesscatterplot3dSeqinfoshinyshinyjssnowsolriumsourcetoolsstringistringrsubplexsystaxizetibbletidyselectTreeDistTreeToolstriebeardurltoolsutf8vctrsviridisLitewhiskerWikipediRwikitaxawithrworrmsXMLxml2xtableXVectorzoo

phruta behind the scenes
General acknowledgements
Rendered frompackage_acknowledgements.Rmdusingknitr::rmarkdown

Last update: 2023-05-02
Started: 2023-05-02

Advanced methods
Table of Contents | Working with non-animal nor plant groups in phruta | Creating taxonomic constraints in phruta | ingroup + outgroup | Particular clades | Running PartitionFinder in phruta | Partitioned analyses in RAxML | Identifying rogue taxa
Rendered fromPhruta_advanced.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2021-08-24

Future directions for phruta
Future directions for phruta
Rendered fromFuture_phruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-05-30

Getting started with phruta
Table of Contents | phruta en Español | What is phruta? | Functions in phruta
Rendered fromphruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-06-29

Phylogenetics with phruta
Table of Contents | Installing RAxML | Installing PATHd-8 and treePL | Phylogenetic inference with phruta and RAxML | Tree dating in phruta
Rendered fromPhylogenetics_phruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-05-30

To export or not export phruta outputs
Table of Contents | To export or not export from phruta | From taxonomic names to sequence alignments, exporting data
Rendered fromExporting_data_phruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-06-02

Usando el paquete de R phruta
Table of Contents | Desde nombres taxonomicos a alineamientos | Guardando objetos intermedios
Rendered fromusando_phruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-06-29

Using phruta with a defined set of target genes
Rendered fromphruta_targetgenes.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-06-28

Using the phruta R package
Table of Contents | Intro tutorial: Clade names to sequence alignments | Saving intermediate files
Rendered fromUsing_phruta.Rmdusingknitr::rmarkdown

Last update: 2023-01-06
Started: 2022-06-02