This is how I downloaded, compiled and got FastTree working. Its a bit obvious in places but I think detailed instructions are a good thing to have out there and Google findable. I am using a multicore MacPro 2.8GHz with 4GB RAM and OSX 10.5.4 (I’m not sure the 8 cores make any difference whatsoever…
Tag: phylogenetics
Actual Science…
So when I started writing this blog I thought I would use it to outline some of the things I was working on as I went along. Not real projects, which I will write up and publish, but side projects and how I got them to work (or otherwise). Unfortunately there hasn’t been much of that,…
Inheritance of phylogenetic methods
I just scanned through a very interesting article in BMC Bioinformatics discussing the results of a data mining approach to describing phylogenetic methodology in published articles. Eales et al. Methodology capture: discriminating between the “best” and the rest of community practice. BMC Bioinformatics 2008, 9:359 doi:10.1186/1471-2105-9-359 They searched for “phylogen*” in titles and abstracts at…
Confident in your phylogeny?
There has been discussion and research for decades into support values for phylogenetic nodes and the relative quality of different phylogenies as a whole. Here is a new and impressive (although clearly subjective) criteria for confidence in a phylogenetic tree- “I am so confident in this tree I have had it tattooed onto my body”!!!The…
FastTree
There was a message on the excellent EvolDir mailing list a few days ago about FastTree. This is a very fast neighbor-joining program for very large scale phylogenetic analyses. It uses profiles rather than a distance matrix and includes local support values instead of bootstraps. The examples in the preprint manuscript talk about datasets of…
phylogenomics?
While I was reading the Nature paper I was talking about in my last post I was thinking about the use of the term “phylogenomics”. It seems like there are two quite separate contexts where it is used.(1) Integrating evolutionary biology into genomics (2) phylogenetics using a lot of data The term “phylogenomics” was first…
The Animal Tree of Life
There’s an interesting paper in Nature on animal phylogeny. The authors take an EST approach adding multi-gene data for 11 new animal phyla and increasing data for others. Dunn et al. “Broad phylogenomic sampling improves resolution of the animal tree of life” Nature. Published online 5 March 2008 doi:10.1038/nature06614 Abstract: Long-held ideas regarding the evolutionary…
SupraMap- Google Earth Trees
I came across SupraMap today. This is a way to overlay phylogenetic trees onto Google Earth images and examine the geographic distribution of the OTUs. Although there have been several postings before at iPhylo, and CIPRES and an implementation for Mesquite, the work at SupraMap looks quite polished. There is a video, and detailed instructions…
ARB- a phylogenetic environment
ARB is a database program for sequence data, alignments and trees. It is primarily used by the microbial rDNA community, although it is equally powerful for other genes and taxonomic groups. ARB is my primary productivity software for phylogenetics and I thought I would introduce it briefly. “The ARB software is a graphically oriented package…
Understanding Evolutionary Trees
Following some links on other blogs I’ve recently seen an excellent article by T. Ryan Gregory called “Understanding Evolutionary Trees”. It introduces and explains evolutionary (phylogenetic) trees and highlights the importance of tree thinking. It even has a section on how NOT to read evolutionary trees, outlining common misunderstandings, misconceptions and misinterpretations. I wish I…
EvoPhylo 