We are happy to announce the release of mothur v.1.24.0! In this release we have three new commands that we think you’ll find useful. Perhaps the most significant is the addition of otu.association, which will use a shared or relabund file to create a matrix of correlation values indicating the association between different OTUs. Just remember that association is not the same as causation :). We’ve also added classify.tree which will take a tree and classification data as input and will output the consensus taxonomy at each node and sort.seqs, which will sort files for you. We’ve also added a number of important feature updates including the addition of p-values to the output from corr.axes. We are very much indebted to the great feedback we’ve been getting through the forum and this feedback is the inspiration of many of the newest commands and features that we’ve added. Thanks!
As I emailed you earlier in the month we’ve also made a number of project-related changes. First, you can now pull down the bleeding-edge version of mothur whenever you want via GitHub. We look forward to more interaction with other developers and hope this will foster even greater collaboration. Second, we’ve added the new RDP training sets. In the next release, look for a command that will allow you to trim the training set sequences to only include the region you are interested in. Also, be on the lookout in the next few weeks for an updated SILVA reference alignment.
Keep the mothur citations coming and you know where to send the six packs!
- otu.association - calculate the correlation coefficient between the otus in a shared/relabund file.
- sort.seqs - puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
- classify.tree - finds the consensus taxonomy for each tree node’s descendants.
- merge.groups - added group option - https://forum.mothur.org/viewtopic.php?f=5&t=1436#p3586
- classify.seqs - mothur will now check to see if the sequence is reversed before classifying.
- fastq.info - added fasta and qfile parameters - https://forum.mothur.org/viewtopic.php?f=5&t=1444
- corr.axes - added p_values
- remove.groups and get.groups - added design file
- trim.seqs and trim.flows - added ldiffs and sdiffs options. You can now include linker and spacer information in the oligos file.
- trim.seqs - added keepforward option, allows you to identify but not remove the forward primer. Default=F.
- filter.seqs, trim.seqs, screen.seqs, pairwise.seqs, dist.shared, metastats and summary.shared - paralellized for windows
- sffinfo - flow default changed to true, added a warning about corrupted sff files.
- classify.otu - if your input taxonomy file contained confidence scores with decimal points mothur failed to remove them before adding classify.otus confidences (was in 1.23.1).
- classify.seqs - knn method was eliminating sequences that could not be classified at the kingdom level. Now they are classified to “unknown”. - https://forum.mothur.org/viewtopic.php?f=4&t=1435
- fixed name of npshannon - https://forum.mothur.org/viewtopic.php?f=4&t=1449
- https://forum.mothur.org/viewtopic.php?f=3&t=1469&p=3719#p3719 - put the full path names into the flow.files file.
- trim.flows - was not trimming the fasta output - https://forum.mothur.org/viewtopic.php?f=4&t=1491&p=3784#p3784
- summary.seqs - in windows version, with multiple processors, occasionally you would get a crash.
- rarefaction.single - group names parsing issue if your group names contain ‘.’ and groupmode=t.
- Uploaded new version 7 of RDP classification
- We now provide a public version of the code repository on GitHub under the name mothur