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…
Author: Dave Lunt
TreeGradients
I came across a nice program by Heroen Verbruggen called TreeGradients. “TreeGradients is a tree drawing program. The tree drawing options are fairly basic but the program has the ability to plot several types of continuous variables at the nodes in colors and use linear color gradients to fill the branches between nodes. The output…
SWAMI and the CIPRES portal
CIPRES may be about to have a data handling overhaul. If you haven’t clicked around on the CIPRES site do so, its great. Cyberinfrastructure for Phylogenetic Research (CIPRES) project is an open collaboration funded by the National Science Foundation…The goal of the CIPRES project is to enable large-scale phylogenetic reconstructions on a scale that will…
Species numbers
Christopher Taylor at the excellent Catalogue of Organisms has a thought provoking post on the taxonomic diversity of described species. He has a picture of animal groups, plants and fungi scaled by number of described species. I like these sorts of pictures; they are great for shocking undergraduates who have never really thought about the…
DropBox and data syncs
I’ve written previously on struggles with data management and looking for ways to keep good electronic records. I recently discovered DropBox. It synchronises all data placed in the local dropbox folder between multiple subscribed Mac/PC machines. Syncing is in real-time (i.e. continuous not periodically scheduled) and very fast. A copy of the contents of your…
Genetic tests of ancient asexuality
I’ve just had a manuscript published at BMC Evolutionary Biology so thought I’d share a synopsis.I’ve been interested in root knot nematodes for a while as they are a powerful system for evolutionary genetics and amazingly successful parasites of plants- especially crop plants. Trudgill and Blok (2001) estimate that they “have host ranges that encompass…
Natural Selection Pie
Today is the 150th anniversary of the presentation of the work of Darwin and Wallace at the Linnean Society. Tell somebody about it, just one extra person. Simple things like this make all the difference. Many people might be surprised to hear that natural selection and evolutionary biology form the core of much of modern…
The Ernst Haeckel Stadium
Just watched Spain win the Euro2008 football final in the Ernst Haeckel stadium, Austria. I was really pleased that Haeckel, evolutionary biologist and artist, originator of the term “phylogeny” and many other key concepts, has been honoured with a football stadium in his name. Sadly a bit of Googling has revealed that it is the…
Perl scripts for phylogenetics
The script I referred to in my last post is actually seqConverter.pl written by Olaf Bininda-Emonds, with a few minor modifications to send the output directly to phyml. I thought I would flag up his site which has a large and very useful collection of perl scripts for phylogenetic data wrangling. These are open-source scripts…
Droppable applications from scripts
I’m not a very competent perl programmer. Even writing the word programmer here makes me slightly embarrassed. I do carry out frequent sequence conversions and manipulations with perl scripts I’ve put together though. Sometimes when I need to run a script many times I’ve found the most irritating thing is launching the scripts and pointing…
EvoPhylo 