Tree Building, part 1

November 21, 2011

For those of you who have actually been reading and are curious, my BLAST finally finished. It only took 9 days, which was nice considering I’ve heard BLAST’s of that size can take months. Finally finished running the myriad programs required to extract data from the proteomes on Friday… and now I’m trying to figure out where and how to utilize this data so I can actually get meaningful info from it.
Beside that, I’m currently working on building a phylogenetic tree using the genomes of the same Archaea I just did BLAST’s of. This tree building is the first part of my actual project for the lab, and I’m pretty excited about it. We’ve decided to use codons to build the tree, which is very time intensive but incredibly accurate and reliable. But, as happens a lot in this field, the software we’re using to build the tree doesn’t support codon models; more specifically, they convert nucleotide models to codon models, but the way in which they do this is less accurate than just using a codon model. So I’ve been tasked with figuring out how to modify the script the software uses to allow us to use the Goldman-Yang (1994) Codon Substitution model. So at the moment I find myself staring at XML scripts and Goldman and Yang (1994) to see what needs to be modified, how, and why. Yay…‽
Hopefully more to come soon.

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