mothur v.1.1.0

We are happy to release mothur v.1.1.0 today, March 9, 2009. In the past 3 weeks we have had 136 people register as users of mothur - thank you for your continued support! Instead of waiting you wait for gigantic buggy versions of mothur (ahem, Bill Gates), our approach will be to make more frequent smaller releases. For the time being, our goal is to focus on adding major features. In the first release it was to include the functionality of dotur and sons. This time around it is the functionality of treeclimber and the UniFrac stable of tools. The next release should include an implementation of slibshuff. Along the way we hope to add minor features that improve the usability of the code.

Over the past several weeks several of you have suggested various features and we appreciate that feedback. Perhaps more surprising has been the interest in having me come to your campuses to give workshops. I am currently looking forward to workshops at Louisiana State University, University of British Columbia, Penn State University, and University of Hawaii. If we have 10-15 people at each workshop, then we will have trained at least 50 people, which is phenomenal. I am also thinking about hosting a workshop at the University of Massachusetts. If you are interested in coming to that workshop, please let me know what dates might be most appealing to you.

Finally, here are a list of the modifications and features that are included in the March 2009 release of mothur v.1.1.0...

Cosmetic Changes

• Better type checking on option parameters
• Don’t need a space between comma and options
• Don’t need to put a quit() command at the end of a batch file
• The collect.single, collect.shared, rarefaction.single, summary.single and shared.summary all use the calc parameter.
• All estimator names are lowercase.
• Only filename parameters persist between commands, all others return to default values.

Major Feature Additions

• unique.seqs
• parsimony
• unifrac.weighted
• unifrac.unweighted
• The shared option to the read.otu command

Minor Feature Additions

• Ability to set comparisons for the collect.shared, rarefaction.shared, and summary.shared commands.
• Ability to define the threshold for “abundant” species in ACE estimator as something other than 10 in the collect.single, summary.single, and rarefaction.single commands.
• Added the get.line, get.group, and get.label commands so basic information about data files can be accessed through mothur.