The New York Times has an article talking about constructing and especially visualizing the tree of life called “Crunching the Data for the Tree of Life“. Its interesting, especially since I think it touches on many issues concerning tree size that even phylogenetic biologists haven’t really considered. There are lots of talk of “big” trees,…
Tag: treeviewers
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…
Google Maps and Phylogenies
Following on from my previous post I decide to try Google Maps as an interface to large phylogenetic trees. This was a very quick and dirty go at seeing whether it would work as a navigable interface. I tried the implementation at MapLib which allows you to upload your own images and use Google Maps…
Genome Projector for trees?
It seems that Genome Projector has swept the blogosphere over the last 24 hours. I’ve seen it listed on many of the blogs I’m reading. It looks very good and intuitive. I just wanted to mention a couple of things.This is a beautiful example of what happens when open source software is championed. Google maps…
Annotating trees with Treedyn
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…
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…
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…
EvoPhylo 