In order to really get information out of building phylogenetic trees (especially large ones) some thought has to be given to how to annotate the tips (OTUs).The two programs that seem to do this in a powerful way are ARB and Treedyn. I also want to explore Tree-Q vista, which looks promising, but haven’t really…
Author: Dave Lunt
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…
Beer and Publications
OK, so I was going to write about bioinformatics and phylogenetics in this blog, and here is my second post already that ignores both!I just read a paper testing the relationship between beer consumption and publication output of ecologists in the Czech Republic. Apparently the higher your consumption the lower your total number of publications,…
How to visualize a phylogeny with thousands of tips?
What abilities should a phylogenetic visualisation tool have? What is important when you have so many tips (OTUs) that it is too big to print out or even scroll through on the screen? I have several pieces of research in this last category. In no particular order here are some things that seem important to…
The Origins of Genome Architecture- Lynch
So I don’t hate all books. Over Christmas I read Michael Lynch’s new book “The Origins of Genome Architecture”. One of the best books I have read in a long time. Well-written, clearly argued, well referenced and important. If you like molecular evolution, genomics or related topics you should definitely read this. I learned a…
Are books now obsolete?
Well no, I guess they’re not. But I’ve been thinking about whether some types of book publishing are even worthwhile. So, what’s my complaint? Well, in many cases I don’t see why either publishers or paper books are of any use. I think researchers can easily self-publish PDFs that are open access, free and may…
SILVA 93 released
The rDNA database SILVA has a new release- SILVA 93.More sequences and some new tools have been added.Metazoa now contains 21,901 accession numbers.[eukarya 83,915, all domains 563,587]
20,000 leaves on my tree
Apologies to Jules Verne, but on 30.10.07 there were 20,363 Metazoan SSU rDNA accession numbers in the Silva 92 database. My immediate questions- can a reliable phylogeny be constructed from this by a biologist with average computing resources? Can the resulting tree be informative (or is it too big to get any meaningful information onto…
EvoPhylo 