mothur v.1.11.0

In honor of the upcoming fathur’s day weekend we are happy to release mothur v.1.11.0. We are working on a number of things behind the scenes that aren’t quite ready for primetime, so this is a relatively light release consisting primarily of feature updates and bug fixes. We think you’ll find the feature updates go along way to expanding the flexibility of existing commands and making them more computationally and memory efficient. Two new commands have been added - split.abund and classify.otu. The split.abund command will allow you to partition your unique sequences based on how many sequences they represent. This could be useful for people interested in using abundant sequences as a reference template for different chimera checking algorithms. The classify.otu command marries the phylotype and OTU-based approaches. Give this command a taxonomy file for your sequences and your list file and for each OTU it will output the consensus taxonomy for the sequences in that OTU. There are several options available for defining what is meant by consensus. Some of you may have missed the last several releases because of difficulties we were having with sending emails out of our server - this should be fixed. Regardless, you should probably take a look at the last several release notes to see how far we have come in the last few months.

Finally, we are trying to gauge people’s interest in attending a workshop on August 23-25 at a hotel near the Detroit airport (DTW). Feel free to email us (mothur.bugs\@gmail.com) if you are interested or have any questions.

New commands

• added split.abund command - split sequence names into abundant and rare categories based on how many sequences they represent in a name file
• added classify.otu command - get a consensus taxonomy for each OTU

Feature updates

• modified chop.seqs command by changing parameter to fasta, keep and numbases. also made it work with aligned sequences.
• added additional file checks to template and taxonomy files for classify.seqs command, - be sure to remove your old .tree.train, tree.sum, .numNonZero, and .prob files
• added taxonomy file to list of files list.seqs, get.seqs and remove.seqs commands can process.
• get.seqs and remove.seqs commands can now process more than one file at a time.
• added dups parameter to get.seqs
• added sort option to get.otulist command - https://forum.mothur.org/viewtopic.php?f=3&t=368&sid=e81f0982fd4e09a24a2aff4ff1cde1c9
• allow for ‘>’ in sequence names
• reduced memory used to generate chimera.pintail commands quantile values by 65%.

Bug fixes

• fixed bug filter.seqs command in mpi enabled version that occasionally caused bus error occurred if trump parameter was used and vertical was set to false and soft was not set.
• fixed bug in trim.seqs introduced in 1.10.0 with the addition of bdiffs, pdiffs and tdiffs.
• fixed with classify.seqs if the taxonomy and template files are in a different folders
• mothur can now read trees generated by fasttree
• fixed bug with chimera.pintail that caused a bad_alloc if the quantiles needed to be generated.