A R package to determine oligotypes from DNA sequences. The package provides R scripts to perform the oligotyping approach (http://oligotyping.org), as a way to exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene sequences.
The R package is presented in: Ramette and Buttigieg, "The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data", Front. Microbiol., 14 November 2014 | doi: 10.3389/fmicb.2014.00601 http://journal.frontiersin.org/article/10.3389/fmicb.2014.00601/full
The original oligotype paper is described in: Eren et al. 2013 Methods in Ecology and Evolution. 4,1111-1119. doi: 10.1111/2041-210X.12114. http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12114/pdf
A) Assuming the file "otu2ot_1.4.tar.gz" is in the directory "C:/R/oligotyping/", type in your R console:
setwd("C:/R/oligotyping/")
install.packages("otu2ot_1.4.tar.gz", repos = NULL, type = "source")
library(otu2ot)
help(otu2ot)
B) A faster way:
library(devtools)
install_github("aramette/otu2ot")