Tuesday, April 07, 2009

Building trees ...

... for my upcoming manuscript. Not enough room in the paper itself (already have 4 tables and 6 figures) so they're going in as Supplemental Material, but that doesn't make it any easier ... seeing as I have over 600 OTUs in my study.

One thing that's nice about Geneious though, you can color coordinate the branches, which is a nice feature when you want to highlight particular clades (which I want to do).

7 comments:

Mad Hatter said...

Hmm...never used Geneious before. Do you like it? I made my trees using ClustalX and TreeView, and then imported them into Illustrator to color as I please. What method are you using, by the way?

Thomas Joseph said...

Hi MH.

I use MUSCLE (available in Geneious) for alignments(Geneious also has their own aligner, but it isn't as robust ... and they also allow ClustalW as well as a couple others). For tree building in Geneious, I typically use PAUP (need to own it before using the Geneious plugin), though their own tree builder is pretty good (basic NJ or UPGMA) and they also provide PhyML. If I were going to put these trees in the actual manuscript itself, I'd probably use MEGA (can export your alignments in FastA format) which is what I've done most of tree building on prior to getting Geneious.

I do love Geneious though. Their programmers work with their customers on a daily basis (via messageboard) and they're always upgrading based on customer requests. It's a multifunctional program as well, and allows you to interface with several major databases. It's not as proficient (currently) for genome-level contig alignments as say, Sequencher, but it's getting there. They also allow you to buy software time on supercomputers so you can out source some of your more major time, and CPU intensive projects.

Mad Hatter said...

"they also allow you to buy software time on supercomputers"

That is totally awesome because my POS computer won't tblastx anything longer than about 500bp without giving me a "CPU usage exceeded" error message!

Thomas Joseph said...

Have you considered converting your POS computer to linux and installing your own BLAST server on it?

Mad Hatter said...

Haven't, but as you know from my blog, I'm pretty much a computer idiot. We do have several server clusters on campus that can be used for this kind of analysis, but that usually entails me asking for favors from the people who have access to the clusters. Will look into this idea with IT.

Thomas Joseph said...

Geneious also allows you to set up a local blast station on your computer. However ... have you looked into MG-RAST? I'm not sure if MG-RAST does tblastx, but it will do blast analysis of your uploaded sequences.

Mad Hatter said...

Actually, I just found out my boss is going to buy the lab a new high-end computer for all this data analysis. Hopefully this will fix all the problems!