Phylogenetic Placement for Inferring Taxonomy (PPIT) is an R package for inferring microbial taxonomy from nifH amplicons. PPIT provides a higher proportion of correct taxonomic inferences at all taxonomic ranks in comparison to BLAST-based approaches at the cost of fewer total inferences.

Installation

To install ppit directly from RStudio, first download the dependent package Biostrings from Bioconductor then use the devtools package to install ppit:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

devtools::install_github("BKapili/ppit")

Documentation

To get started, see the tutorial that walks through the analysis using nifH amplicons generated from Illumina MiSeq data.