phylotypr is a package for classification based analysis of DNAsequences. This package primarily implements Naive Bayesian Classifierfrom the Ribosomal Database Project. Although you can classify any typeof sequence (assuming you have the proper database), this algorithm ismainly used to classify 16S rRNA gene sequences.
You can install the development version of phylotypr fromGitHub with:
# install.packages("devtools")devtools::install_github("mothur/phylotypr")You can also get the official release version from CRAN
install.packages("phylotypr")Be sure to see theGettingStarted article to see an example of how you would build thedatabase and classify individual and multiple sequences.
The{phylotypr} package ships with the RDP’s v.9 oftheir training data. This is relatively small and old (2010) relative totheir latest versions. You are encouraged to install newer versions ofthe RDP, greengenes, and SILVA databases from the{phylotyprrefdata} package on GitHub. Note that installingthe package will take about 20 minutes to install. If it sits at “movingdatasets to lazyload DB” for a long time, this is normal :)
devtools::install_github("mothur/phylotyprrefdata")library(phylotyprrefdata)The following will list the references that are available in{phylotyprrefdata}:
data(package ="phylotyprrefdata"){phylotypr}You can learn more about the underlying algorithm in the paper thatoriginally described the algorithm that was published inApplied andEnvironmental Microbiology. If you want to learn more about howthis package was created, be sure to check out the mothur YouTubechannel where aplaylistis available showing every step.