Mor Development Blog

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updates and streamlining

Posted by Tom Heider (2008-06-26 13:11:00)

We're currently in the process of simplifying, streamlining synergizing and slickifying mor. What that means is we're doing some rewrites on mor to generalize it so it can maintain more complete records of different genes in a mySQL table. A positive side effect of that is that it will be much simpler to create your own instance of mor because it will require less code to understand and be easier to follow what is happening. The effect of all these changes is that mor will have a better record of the downloaded sequences. This means that we will be able start implementing the two other mor projects for this summer, a super tree analysis (super mor) and one other function that we're going to keep you in suspense about.

maximum likelihood tree and downloadable package

Posted by Chuck Ha (2008-06-17 13:33:00)

Tom and I have finally packaged up mor and made it available for download! Please be sure to read the included README file with instructions for installation.
But that's not all. After adding RAxML to the mor program we are now able to publish a maximum likelihood tree along with the parsimony tree and the jackknife neighbor-joining tree!
Be on the look out for even more updates coming soon.

New Backbone Tree and Package Update

Posted by Tom Heider (2008-06-11 04:30:00)

We're still at work on mor here in the Hibbett lab and we've given mor the new backbone constraint tree that Professor Hibbett supplied to us earlier this summer. We've implemented MAFFT and RAxML into shadow mor so now all we're doing is testing them to see how they work before updating mor.

For those of you interested in getting mor operational in your lab, you'll be glad to know that Chuck is hard at work setting up the necessary files. Any sort of delays in putting the package online for download is to make sure the program is in a usable state (ie doesn't take more than a week to run on your machine) with useful install instructions (ie doesn't take more than a week to install on your machine).

Forward Movement

Posted by Tom Heider (2008-06-04 10:20:00)

We now have mor up and running on an automated basis, so you can now look forward to seeing updates to the trees and alignments. We also have managed to set up shadow mor, which we're currently putting through its paces. What that means for you is we'll be able to make changes to the mor codebase while not having to take mor offline for an extended period of time. Our next step is to package up all the mor scripts with some instructions on what to do with the package so that you'll be able to create your own implementation of mor.

We've also done some tests with MAFFT and RAxML and both programs have preformed extremely well with the mor dataset. With approximately 3,000 accepted sequences MAFFT was able to do a profile alignment in under 10 minutes, while clustalw takes two days to add do that. RAxML has also been able to create a tree using ML in under two days while PAUP*'s settings are for five days for a MP tree. For us, this means that Chuck and I will be writing wrappers for those two programs for shadow mor and for you, this means once we're done, mor will be a much more practical project to be implemented.

First day of summer progress

Posted by Tom Heider (2008-05-27 16:20:00)

I would like to welcome Chuck Ha to the development team for mor. He’s a student at Clark University and will be working with me on fine tuning some aspects of mor and turning it into a finished piece of software.

We’re currently working on the automation of mor and are fairly close to getting it back up and running like it used to be. We also have a couple enhancements that I’m particularly excited to add to mor beyond the basic bug fixes. Come back later this week and either Chuck or I will give you another update on what is happening with mor now that there are two people working full time on it.