Monday, January 24, 2011

Phylogeny rules:

I am a coauthor on a new paper in PLoS Computational Biology I thought I would promote here.  The full citation for the paper is:

The paper discusses a new software program "phylOTU" which is for phylogenetic-based identification of "operational taxonomic units", which are also known as OTUs.   What are OTUs?  They are basically clusters of closely related sequences that are used to represent something akin to a species.  OTUs are used a lot in environmental microbiology b/c one key way to study microbes in the environment is through extraction and sequencing of DNA.  Traditionally this has been done through PCR amplification and sequencing of one particular gene (ss-rRNA).  Now it is also being done through random sequencing of all DNA from environmental samples (so called metagenomics).

Anyway - the paper is (of course) fully open access and you can read it for more detail.  Just thought I would post a little here about it.  The paper / project was led by Tom Sharpton, a post doc in Katie Pollard's lab at UCSF working on a collaborative project between Katie's lab, my lab, and Jessica Green's lab at U. Oregon (and recently Martin Wu's new lab at U. Virginia - he was in my lab previously).  This collaborative project even has a name "iSEEM" which stands for integrating statistical, evolutionary and ecological approaches to metagenomics.  This project has been generously supported by the Gordon and Betty Moore Foundation (via a grant for which I am PI).
Some little tidbits of possible interest about the project

Sharpton, T., Riesenfeld, S., Kembel, S., Ladau, J., O'Dwyer, J., Green, J., Eisen, J., & Pollard, K. (2011). PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data PLoS Computational Biology, 7 (1) DOI: 10.1371/journal.pcbi.1001061


  1. Using Infernal! I heartily approve. Did you try ssu-align also by Sean Eddy and Eric Nawrocki? It's based on infernal but much faster...

  2. we have been playing a lot with SSU-align --- not sure if Sharpton has incorporated it into phylOTU

    1. Hey Jonathan, I needed some help with using the ssu-mask in the ssu-align software.
      my e-mail :

      Do reply to my e-mail id, I will mail you exactly what problem I have.


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