mothur v.1.3.0

We are happy to release mothur v.1.3.0 today, May 25, 2009. Since the April release we have added an additional nearly 100 users. Thanks to the 347 of you for your continued support! It was great to meet so many people at the 2009 ASM General Meeting in Philadelphia, PA and to hear what people are up to. The skinny on my poster is that I reanalyzed the Sogin pyrosequencing dataset of 222,000 V6 tags in under 6 hrs on my Mac laptop. Most of that time was spent calculating the pairwise distances, which we have parallelized so you can use up to 4 processors.

This release gets us ever closer to having a complete pyrosequencing pipeline. We have added tools to filter out user-specified columns from an alignment file, calculate pairwise distances from an alignment file using multiple processors, generate a pairwise distance matrix and newick-formatted tree to describe the similarity between communities. We have added an additional four calculators, which predict the number of additional OTUs that would be observed with further sampling and we have made use of Anne Chao’s recent modifications to the shared Chao estimator to estimate the shared richness between two or more communities. For those of you using batch files, it is now possible to annotate your file with comments by making the first character of a line ‘#’. Finally, we have tried to iron out a few pesky bugs. Looking forward to the Fathur’s Day release, we are planning on introducing an aligner that is as good or better than the SILVA, NAST, or RDP aligners, but considerably faster plus a number of additional features. If you would like to help us evaluate the aligner, please email me.

Those of you that have been with us since February know that I have been engaged in two open-source experiments. First, in the last release I mentioned that if people made a substantive contribution to the wiki or contribute code, then I would include them as a co-author on the mothur manuscript that I will submit this summer. several people have taken me up on this by generating wiki pages describing how they have used mothur and other tools to analyze their data. If you are interested in contributing and being a co-author, please make your contribution by July 1. Please email me with any questions. Second, I have made myself an open-source resource by providing workshops free of charge (except my travel expenses). I’m about to go to the University of British Columbia for a workshop and later in the summer I’ll be at the Microbial Diversity course at Woods Hole and then Penn State University. If you are interested in coming to Amherst to participate in the workshop (and why else would you come to Amherst?) please let me know. I’m thinking of offering the workshop here in July. If you’re thinking of flying - the closest airport is Hartford, CT (BDL), which is about an hour away.

My apologies to those of you looking for . mothur’s Day release earlier in May. It was a golden opportunity to further milk the name, but so it goes. But you can look forward to a Fathur’s Day release.

Minor updates

Major updates

  • The filter.seqs command - Remove select columns from an alignment by removing any column that has a specific character in it, a minimum base frequency, or a user-supplied filter
  • The dist.seqs command - Generate a column-formatted sequence-based pairwise distance matrix
  • The dist.shared command - Generate a phylip-formatted community-based pairwise distance matrix
  • The tree.shared command - Generate a newick-formatted tree file comparing the membership or structure of multiple communities


  • sharedchao - updated richness estimator for N≥2; incorporated into calculating 3- and 4-way Venn diagrams
  • boneh - Boneh’s estimator to determine how many how many new species would be observed with additional sampling
  • efron - Efron’s estimator to determine how many how many new species would be observed with additional sampling
  • shen - Shen’s estimator to determine how many how many new species would be observed with additional sampling
  • solow - Solow’s estimator to determine how many how many new species would be observed with additional sampling

Bug fixes

  • Got rid of weird output to screen when running collect.single or using the npshannon calculator
  • Fixed bug that would not permit freq=1
  • Fixed file error with rarefaction.single and rarefaction.shared
  • Fixed how scaling worked on heatmap
  • Patched up a number of memory leaks and other memory problems
  • Modified many of the *.shared commands to be much faster