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

# Install 'phruta' in R:

install.packages('phruta', repos = c('https://packages.ropensci.org', '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:

5.21 score 9 stars 20 scripts 13 exports 150 dependencies

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

Target	Result	Time
linux-devel-x86_64	ERROR	613
pkgdown docs	OK	233
source / vignettes	OK	281
linux-release-x86_64	ERROR	519
macos-release-arm64	ERROR	489
macos-oldrel-arm64	ERROR	382
windows-devel	ERROR	480
windows-release	NOTE	587
windows-oldrel	ERROR	578
wasm-release	OK	185

Exports:acc.table.retrieve gene.sampling.retrieve getListConstraints sq.add sq.aln sq.curate sq.partitionfinderv1 sq.retrieve.direct sq.retrieve.indirect tree.constraint tree.dating tree.raxml tree.roguetaxa

Dependencies:apcluster ape askpass base64enc BiocGenerics Biostrings bit bit64 bslib cachem class cli clusterGeneration coda codetools colorspace combinat commonmark cpp11 crayon crul curl data.table DBI DECIPHER DEoptim deSolve digest doParallel doSNOW dplyr e1071 expm farver fastmap fastmatch fontawesome foreach fs geiger generics ggplot2 glue gtable hms htmltools httpcode httpuv httr igraph ips IRanges isoband iterators jquerylib jsonlite kebabs kernlab labeling later lattice lazyeval LiblineaR lifecycle magrittr maps MASS Matrix matrixStats mclust memoise mime mnormt msa mvtnorm natserv ncbit nlme numDeriv oai odseq openssl optimParallel otel pbapply phangorn phytools pillar pkgconfig PlotTools plyr prettyunits progress promises proxy quadprog R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppParallel Rdpack rentrez reutils Rfast rgbif ritis rlang rncl Rogue rotl rredlist S4Vectors S7 sass scales scatterplot3d Seqinfo shiny shinyjs snow solrium sourcetools stringi stringr subplex sys taxize tibble tidyselect TreeDist TreeTools triebeard urltools utf8 vctrs viridisLite whisker WikipediR wikitaxa withr worrms XML xml2 xtable XVector zigg zoo

Advanced methods

Rendered fromPhruta_advanced.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Future directions for phruta

Cristian Román-Palacios

Rendered fromFuture_phruta.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Getting started with phruta

Rendered fromphruta.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

phruta behind the scenes

Cristian Román-Palacios

Rendered frompackage_acknowledgements.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Phylogenetics with phruta

Rendered fromPhylogenetics_phruta.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

To export or not export phruta outputs

Rendered fromExporting_data_phruta.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Usando el paquete de R phruta

Rendered fromusando_phruta.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Using phruta with a defined set of target genes

Rendered fromphruta_targetgenes.Rmdusingknitr::rmarkdownon Apr 08 2026.

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

Using the phruta R package

Rendered fromUsing_phruta.Rmdusingknitr::rmarkdownon Apr 08 2026.