Just before Christmas I went to the 42nd Population Genetics Group conference (“PopGroup”) in Cardiff. This is my favourite scientific meeting and is a real institution in the UK. Its not really population genetics as understood today, although it includes popgen, rather evolutionary genetics in a broad sense. I’ve always thought that this title just…
Author: Dave Lunt
career success
I enjoyed this cartoon from xkcd (via genetic future).
FastTree 3: Timing some runs
I downloaded some datasets from the SILVA96 database. These are structurally aligned SSU rDNA sequences. I browsed through the taxonomic groups and chose annelids (N=1050) and nematodes (N=5048) as smallish tests. I downloaded these as fasta files. I started with the annelids file. The file contain a LOT of gaps, because it comes from an…
FastTree 2.5: Update
The prediction I made before about a long silence once this year’s students turned up was sadly accurate. Anyway, students dealt with, grant proposal submitted, lectures (mostly) given, bureaucracy reduced (a bit), time to get on with some phylogenetics. I was playing before with FastTree. Although it looks to have been quite well tested by…
FastTree 2: Timing runs
In order to to see how quickly FastTree runs for me I need some automated method of timing it. While some programs like phyML return a runtime at the end FastTree doesn’t seem to. So I searched the web and found bits of perl code to put a script timer together. I have uploaded the…
FastTree 1: Compiling and testing
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…
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,…
Research Culture- lessons from Google?
I just read a post at Mario’s Entangled Bank called “Running an Academic Lab Google Style“. Some interesting ideas that I was aware of but had kind of forgotten. When I was a postdoc I had lots of strong views on how research should be done and although I haven’t really changed my mind it…
Reading the story in DNA
I just received a copy of “Reading the story in DNA; a beginner’s guide to molecular evolution” by Lindell Bromham, OUP 2008, ISBN: 978-0-19-929091-8I have only looked at it quickly but it is very impressive. I like the writing style. It is well produced. Figures are excellent. The parts I have read are full of…
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…
EvoPhylo 