We are happy to announce the release of Mothur v.1.18.0. This is a very significant release, so please pay close attention to the notes below. We have implemented a number of new and important commands and we have significantly improved the usablity of mothur.
Thinking about usability... First, we have reworked how you interface with the commands to hopefully make it much easier to use. Through teaching numerous workshops, I have noticed that the long file names are ridiculous and even I have problems with typos. To counter this, we have improved mothur’s “memory” to make it, um, more motherly. If you start with sffinfo or any other command where you insert a fasta file name, mothur will either guess which fasta file you need for the next command, or you can tell it fasta=current. The same works for name, group, accnos, and taxonomy files. In addition, if you use processors=8, mothur will remember to use 8 processors where possible in all of the other options. Second, all the read commands (e.g. read.dist, read.otu, etc) have been scrapped because they didn’t do anything and were a painful(less) extra step. Instead, you will now enter the information into the actual command you want to run. This has the side effect that we need a new command, make.shared, to parse list files into shared files. Third, if I have a hard time keeping straight what commands use template files and which use reference files, I suspect many of you do as well. To solve this problem, we have streamlined our option names so that any input sequence file uses the fasta option (no more candidate files) and any reference sequence file now uses the reference option (no more template files). If you forget and use candidate and template in align.seqs mothur won’t make a peep.
Thinking about functionality... We just published a paper in Applied and Environmental Microbiology that talks about clustering sequences into OTUs. In that manuscript we describe metrics for assessing clustering quality, this was done using the newly released sens.spec command. We also describe a new method of speeding up and reducing the memory requirements of clustering based on splitting sequences by taxonomy or distance matrices by taxonomy or distance. This functionality is available using the cluster.split command. As part of this paper we have concluded that furthest neighbor needs to go away for most applications. While you can still use the furthest neighbor algorithm (method=furthest), the average neighbor algorithm is the new default. In addition, to simplify everyone’s life, we have abandoned using the rounding option as a default and now use a hard cutoff (cutoff=T). Give the paper a read and if you have any questions, holler.
Please feel free to let us know what you think about these improvements. They really are geared towards making your life easier. Although we resist making such large changes, the further we wait the more wonky things get. I will be implementing these changes to the Costello Data Analysis page over the next few days to show how we would use the new commands with the new version of mothur.
A couple of other small notes... First, there are still spots available in the mothur workshop I will be holding on April 27-29 in Detroit. Second, I will be moving this mailing list and the google group mailing list to a new system so if you don’t want to be on the list you can just pluck yourself off. Third, ahem, the delivery of 6 packs and harder liquor has slowed considerably. You know where to send them...
Till next time,
- cluster.split - A parallelized approach to clustering sequences into OTUs
- sens.spec - A method of determining the quality of OTU assignment
- make.shared - creates a shared file from a list and group file.
- removed read.dist,
commands - you will receive a warning if you use these commands
- you now use the actual command to read in the file
- For example: cluster(column=amazon.dist, name=amazon.names)
- get.current - outputs current files mothur is saving, allows you to clear values.
- set.current - allows you to overwrite mothur’s current files and clear them.
- cluster, hcluster, mgcluster and cluster.split - changed default clustering method to average and set hard to true
- summary.seqs and align.check - added name file option to
- align.check - added summary output information
- screen.seqs - included name file information to improve use of the optimize step
- align.seqs - sped up the merging of files when running with multiple processors.
- get.groups and remove.groups - added group counts info to the output
- normalize.shared - when norm is greater than the number of sequences in a sample it is removed from the analysis
set.current and pretty much every other
command in mothur:
- you can now set filenames to “current”. example: summary.seqs(fasta=stool.fasta) unique.seqs(fasta=current). Also, if a required parameter is not given mothur will look for the current file, so summary.seqs(fasta=stool.fasta) unique.seqs() would also work.
- processors parameter persists, so if you set processors=2 for any command mothur will use 2 processors for all commands that use multiple processors.
- Streamlined option names for input files:
- Input fasta files now all use the fasta option (no more “candidate”, etc.)
- Reference fasta files now all use the reference option (no more “template”, etc.)
- Catchall - fixed bug that caused a bad_alloc after running with a shared file.
- get.lineage and remove.lineage - fixed bug with that caused a crash if your taxonomy file contained confidence scores that were not integers and you requested taxons containing confidence scores.
- clearcut - fixed bug with that caused it not to complete if you requested the version information.
- pca - fixed compute bug
- pairwise.seqs - fixed bug caused by using Nast when aligning.