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. Furthrmore, 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.
phruta is also able to perform basic phylogenetic inference under RAxML on the resulting sequence alignments. The current release allows users to conduct tree dating based on secondary calibrations. phruta is essentially a wrapper for alternative R packages and software.
phruta simplifies the phylogenetic pipeline, increases reproducibility, and helps organizing information used to infer molecular phylogenies.
phruta is currently only available through GitHub. It can be easily installed using the following code.
library(devtools)
install_github("cromanpa94/phruta")
My package is dedicated to my mom and every single Black woman. I still have lots of things to learn from you. You will always have all my admiration and respect.
The logo features a Palenquera in Cartagena (Colombia). For many folks, Palenqueras are just the Black woman ones who sell fruits in particular Colombian turistic areas. However, palenqueras and Palenque are central to Black identity in Colombia, Latin America, and America. "Palenque was the first free African town in the Americas".
Fruta is the Spanish word for Fruit. English ph sounds the same as F in Spanish. In phruta, ph is relative to phylogenetics. I pronounce phruta as fruta in Spanish.
More details about the functions implemented in phruta can be found in the different vignettes associated with the package or in our website.
Please see our contributing guide.
Please see the package DESCRIPTION for package authors.