mothur v.1.2.0

We are happy to release mothur v.1.2.0 today, April 24, 2009. Since our last release we have nearly doubled the number of mothur users. Thanks to the 258 of you for your continued support! This is a very exciting release. First, by making the libshuff algorithm available in mothur, we have now replaced each of our previous tools with a more flexible implementation in mothur. For example, in s-libshuff you needed to sort your matrix prior to input, which was a pain. Now, with the libshuff command this is no longer necessary as you can instead provide a group file. Second, now that we have finished the old stuff, we are moving into newer ventures. In this release we provide four new commands which will enable you to generate heat maps representing rank-abundance data, generate venn diagrams, obtain representative sequences from each OTU, and generate a file that is labelled and sorted according to a list file. Third, we are now ready to start working on a manuscript describing mothur.

I would like you to consider helping me with an experiment. It is very important to me that I engage the broader microbial ecology community in this project. One way that anyone can help out would be to contribute text to the wiki. There are at least three ways that almost anyone could help. First, if you look around our pages you’ll notice a lack of images and references. We are up to about 85 pages on the wiki and I don’t know that I can “beautify” these pages on my own. Second, the pages describing the calculators are very dry and missing from them is a discussion of why one is better than the other and some of the theory that explains what the calculator is trying to do. Third, people learn from example and find it very helpful to copy someone else’s work to learn how to use a piece of software. This month I have posted a page describing an esophageal community analysis. I would love to have more of these pages for people to look at and learn from. But the problem with getting people to contribute to such an endeavor is how to reward and give credit to contributors. So here’s an offer that no junior scientist should turn down. If you make a significant contribution to the wiki, I will add your name to a publication we are preparing that describes mothur. My goal is to submit a manuscript sometime during the summer. By significant contribution, I mean something of the magnitude of a full page or more, not fixing someone else’s typos. Authorship order will be determined by the level of contribution. If you have any questions, please do not hesitate to be in touch.

If you are going to Philadelphia for the 2009 ASM meeting, please stop by our poster, “Introducing mothur: A Computational Toolbox for Describing and Comparing Microbial Communities.” I will be presenting the poster in the Molecular Microbial Ecology - Communities - I session on May 18th at 1:00 PM. The presentation number is N-099. I would love to get your feedback and suggestions. I have benefited enormously by the workshops I have given in the last few months at the University of Massachusetts, University of Wisconsin, and Louisiana State University and am looking forward to visiting with folks at the University of Brittish Columbia, Pennsylvania State University, and possibly Hawaii in the coming months. We are very excited about this project and have a lot of plans for future releases. We are well on our way to implementing a version of the NAST aligner, a distance calculator function, a function to generate dendrograms based on community similarity, and additional calculators.

Major Feature Additions

  • libshuff - carry out a libshuff analysis using the discrete or integral form with a group file
  • heatmap.bin - generate a heatmap of the relative abundance for single or multiple samples
  • venn - generate a Venn diagram using the observed or estimated richness for up to 4 groups
  • bin.seqs - output a fasta-formatted sequence file with the OTU membership for each sequence
  • get.oturep - output a fasta-formatted sequence file with a representative sequence for each OTU

Minor Feature Additions

  • modified read.dist to read matrix for libshuff command
  • New calculators:
    • chao - updated the formulae to reflect what is done in EstimateS
    • logseries - test whether observed data follow the log series distribution
    • geometric - test whether observed data follow the geometric series distribution
    • bstick - tests whether observed data follow the broken stick distribution
    • qstat - the Q Statistic
    • bergerparker - the Berger-Parker index
    • nseqs - the number of sequences in a sample
    • coverage - the coverage of the sample
    • whittaker - the Whittaker similarity index
    • sharednseqs - the number of sequences in the two samples
    • anderberg - the Anderberg index
    • braycurtis - the Bray-Curtis similarity index
    • kulczynski - the Kulczynski index
    • kulczynskicody - the Kulczynski-Cody index
    • lennon - the Lennon similarity index
    • morisitahorn - the Morista-Horn similarity index
    • ochiai - the Ochiai similarity index

Wiki Improvements

  • Added manual calculations and mothur output for all of the calculators available in mothur
  • Added the esophageal community analysis page as an example case study of how to use mothur to analyze community sequence data