Background
Oligotyping [1] was originally developed to detect subtle nucleotide differences in the 16S rRNA gene, which is a non-protein coding gene and functional selection is characterized by strongly conserved regions flanking hypervariable regions that have diverged over evolutionary time. Different patterns of functional selection are observed in protein coding genes, where changes at the third position in the codon are often non-selective due to the degenerated nature of the genetic code, while changes in the first or second nucleotide are likely to produce a change in amino acidic sequence; in some cases this change might result in an increase of fitness or adaptation. Using a high resolution entropy based method like oligotyping or MED [2] on coding sequences can result in the overestimation of the effective genetic diversity in the environment as a result of a much faster evolution rate of the third position in the codon.
In Zure et al. 2016 [3] we developed a set of diagnostics to explore the existence of substitution saturation on the alignments of functional genes that will be used for oligotyping.
Tutorial
A detailed tutorial on how to use oligo4fun can be found here
Installation
Detailed instructions for the installation can be found here
References
[1] Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., and Sogin, M. L. (2013). Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol. 4(12)
[2] Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., & Sogin, M. L. (2015). Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME Journal, 9(4), 968-979
[3] Žure, M., Fernandez-Guerra, A., Munn C. and Harder, J. (2016). Geographic distribution at sub-species resolution level: closely related Rhodopirellula species in European coastal sediment. The ISME Journal. doi:10.1038/ismej.2016.123.