mothur v.1.4.0

We are happy to release mothur v.1.4.0 today, June 21, 2009 (aka Fathur’s Day). Since the May release we have added an additional 120 users. Thanks to the 466 of you for your continued support! We are very excited about this release. With this release you can go from the fna file generated by a pyrosequencer to Venn diagrams in a pretty short period of time, without having to leave mothur. Yes, we have added a function to trim primers off of your sequences and generate a group file based on barcode sequences, align those sequences to any reference alignment you might like, and screen sequences based on their quality and start and end positions. The aligner is parallelized so that you can do your alignment on as many processors as you desire (same goes for the distance calculator, dist.seqs). In addition to a number of other commands, which are described below, we have added options to previous commands. For example, if you request a rarefaction be calculated for a distance of 0.03, but that line doesn’t show up in the *list file, mothur is now smart enough to use the previous line. Another option is the ability to run mothur commands off the command line in what we are calling command line mode. We have also done our best to remove a number of bugs and memory leaks. Please forward us any bugs you encounter along the way. Finally, you should notice a reorganization of the wiki pages so that the command names correspond to the page names.

There are also several news items of note:

  • In the coming months mothur will be moving. I have taken a job at the University of Michigan in the Department of Microbiology & Immunology. Because of this, we have secured the domain and will be moving the mothur wiki to that site in the next month.
  • We received a phenomenal level of interest in the July workshop to be held at the University of Massachusetts - 30 people(!) will be attending. My wife fears that the Tuesday night BBQ will turn into a kegger. I also have received a number of invitations for the Fall and Spring semester. It’s great to see so much interest.
  • The mothur manuscript is written and we have 8 non-UMass co-authors. I consider that a great success for this open source experiment. Feel free to check out their contributions on the analysis examples page. Also, you have until Monday, June 29, to post an example and be included on the manuscript. If you haven’t seen it and think you should be a co-author, please let me know.
  • I have been approached by several people about (i) writing letters of support for proposals, (ii) being a co-PI, (iii) being a subcontractor and (iv) doing people’s analysis for them (for free). Please see the collaboration link on the main page of the wiki for collaboration options.

If you haven’t noticed, we’re very excited about the mothur project and have big plans. Next up on our docket is incorporating a Bellerophon-like chimera checker, a classifier, and the ability to essentially parallelize the cluster command. If you have ideas, please don’t hesitate to get in touch.

Happy Fathur’s Day!

Major updates

  • align.seqs - generates an alignment to a user-supplied template alignment database [pds]
  • summary.seqs - outputs statistics regarding a collection of sequences [pds]
  • screen.seqs - screen sequence and name, group, and/or files based on whether sequences satisfy user-defined criteria [pds]
  • reverse.seqs - outputs the reverse complement of a file of sequences [pds]
  • heatmap.sim - creates a heatmap based on groups similiarity.
  • get.rabund - outputs an rabund file
  • get.sabund - outputs an sabund file
  • trim.seqs - trims and culls sequences based on user-defined criteria, barcodes, and primers
  • merge.files - concatenates a list of files

Minor updates

  • tree.shared command now allows you to input a distance file [sw]
  • added “smart” distance recognition on all commands using the label parameter [sw]
  • added a “name” option to unique.seqs
  • added ability to omit () on the quit command [sw]
  • the deconvolute() command is now called the unique.seqs.
  • the bin.seqs and get.oturep commands now accept a group file. If you provide a group file they will append the group info to the sequence name and bin number [sw]
  • no longer support sequence files in nexus, clustal or phylip form [sw]
  • dist.seqs now has the ability to output a phylip formatted distance in addition to the column format. To do so use the parameter phylip=t [sw]
  • sharedmultiple.summary file is only generated from the summary.shared command when there are more than two samples [sw]
  • dist.seqs can now use n processors.
  • the heatmap command is now called heatmap.bin.
  • modified how the help command is called
  • created the command line mode

Bug fixes

  • fixed infinite loop if mothur is given a non-existent batchfile [sw]
  • fixed command. [sw]
  • optimized summary.shared command [sw]
  • ability to use -1 in a distance file to represent infinity [sw]
  • tree.shared command creates trees with root to tip length of 0.5 [sw]
  • fixed bug where unique.seqs would double the length of the last sequence [ps]
  • fixed bug with read.dist for windows users [sw]
  • fixed help for filter.seqs and align.seqs
  • fixed bug with deconvolute that double the length of last sequence
  • mothur now recognizes TRUE, true, T and t as true.
  • removed using namespace std from all files except mothur.h and defined arrays to comply with C++ standard to better support VS.
  • added and defined math functions for windows user.
  • fixed memory access violation with read.dist.
  • fixed a minor bug in tree.shared command.
  • get.oturep can now process aligned sequences as well as unaligned sequences.

Wiki updates

  • Reorganized the mothur manual
  • Changed page names for commands to be the name of the command (e.g. read.dists is at read.dist)
  • Created a commands category