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-4.5)phruta_0.1.3.zip(r-4.4)
phruta_0.1.3.tgz(r-4.5-any)phruta_0.1.3.tgz(r-4.4-any)phruta_0.1.3.tgz(r-4.3-any)
phruta_0.1.3.tar.gz(r-4.5-noble)phruta_0.1.3.tar.gz(r-4.4-noble)
phruta_0.1.3.tgz(r-4.4-emscripten)
phruta.pdf |phruta.html✨
phruta/json (API)
NEWS

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

On CRAN:

4.75 score 9 stars 14 scripts 13 exports 190 dependencies

Last updated 9 months agofrom:a664f5f2d9 (on main). Checks:1 OK, 6 ERROR, 1 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 14 2025
R-4.5-win	ERROR	Mar 14 2025
R-4.5-mac	ERROR	Mar 14 2025
R-4.5-linux	ERROR	Mar 14 2025
R-4.4-win	ERROR	Mar 14 2025
R-4.4-mac	NOTE	Mar 14 2025
R-4.4-linux	ERROR	Mar 14 2025
R-4.3-mac	ERROR	Mar 14 2025

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 assertthat backports base64enc BiocGenerics Biostrings bit bit64 bitops bslib cachem checkmate class cli clipr cluster clusterGeneration coda codetools colorspace combinat commonmark cpp11 crayon crul curl data.table DBI DECIPHER DEoptim deSolve digest doParallel doSNOW dplyr e1071 evaluate expm fansi farver fastmap fastmatch fontawesome foreach foreign Formula fs geiger generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httpcode httpuv httr igraph ips IRanges isoband iterators jquerylib jsonlite kebabs kernlab knitr labeling later lattice lazyeval LiblineaR lifecycle magrittr maps MASS Matrix matrixStats mclust memoise mgcv mime mnormt msa munsell mvtnorm natserv ncbit nlme nnet numDeriv oai odseq openssl optimParallel pbapply phangorn phytools pillar pkgconfig PlotTools plyr prettyunits progress promises proxy purrr quadprog R.cache R.methodsS3 R.oo R.utils R6 rappdirs ratelimitr rbibutils RColorBrewer Rcpp RcppArmadillo RcppParallel RCurl Rdpack readr rentrez reutils rex Rfast rgbif ritis rlang rmarkdown rncl Rogue rotl rpart rredlist rstudioapi S4Vectors sass scales scatterplot3d shiny shinyjs snow solrium sourcetools stringi stringr subplex sys taxize tibble tidyselect tinytex TreeDist TreeTools triebeard tzdb UCSC.utils urltools utf8 vctrs viridis viridisLite vroom whisker WikidataQueryServiceR WikidataR WikipediR wikitaxa withr wk worrms xfun XML xml2 xtable XVector yaml zigg zoo

Advanced methods

Rendered fromPhruta_advanced.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Future directions for phruta

Cristian Román-Palacios

Rendered fromFuture_phruta.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Getting started with phruta

Rendered fromphruta.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

phruta behind the scenes

Cristian Román-Palacios

Rendered frompackage_acknowledgements.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Phylogenetics with phruta

Rendered fromPhylogenetics_phruta.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

To export or not export phruta outputs

Rendered fromExporting_data_phruta.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Usando el paquete de R phruta

Rendered fromusando_phruta.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Using phruta with a defined set of target genes

Rendered fromphruta_targetgenes.Rmdusingknitr::rmarkdownon Mar 14 2025.

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

Using the phruta R package

Rendered fromUsing_phruta.Rmdusingknitr::rmarkdownon Mar 14 2025.