So, having just built my home machine I wanted to test this (1x Quad 2.83 Ghz) against 1) my work desktop machine with equivalent processors but Xeon (so server chips instead of desktop chips; 2x Quad 3 Ghz) and then I wanted to test against someone’s new Nehalem Xeon server chips (2x Quad 2.66 Ghz [...]
Among the programs I develop, one called phyutility has the largest user base with over 1248 downloads. The original impetus for the development of the program was two fold: 1) to complete some work on the metazoan phylogeny (Dunn et al., 2008) and 2) to complete some work on megaphylogenies (Smith and Donoghue, 2008 and [...]
I have been programming my large dataset assembler program called PHLAWD (another in a series of self-deprecating program names). One step in the algorithm is to compare sequences (pairwise sequence comparisons). Many dataset assemblers employ this step, using maybe a N x N blast procedure or something similar. I make some simplifying assumptions and only [...]
Recently there has been some interest in books with bioinformatics algorithms that would be of interest to evolutionary biology and phylogenetics. So I figured I would list some: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology by Dan Gusfield — a little older but good stuff in here Numerical Recipes 3rd Edition: The [...]
A ramble follows… As previous posts have eluded, I am working on building large trees and the software to do that. I have found out a few things along the way, such as the fact that linux is still better for some things (some would say, quite a lot of things) than mac (especially easy install [...]
So I just finished setting up my new macbook pro. The last thing I installed were some open source apps and libraries. I noticed a few unfortunate things in the process of installing these and that is the poor support and representation (still!) for mac and these products. This includes specifically NumPy, SciPy, and postgresql. [...]
Some colleagues and I (especially Jeremy Beaulieu and Michael Donoghue) have been interested in making large phylogenies. We have been trying to develop (semi) automated methods and implementations that can assemble datasets quickly. The assembly of the phylogeny and matrix itself appears to not be the major computational problem anymore. Although we are sure to [...]
