Big Trees in the NY Times

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,…

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 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,…

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…

SILVA94

There is a new release (94) of the SILVA database of ribosomal DNA sequences. 23,133 Metazoans, 88,997 Eukaryotes and 606,879 SSU sequences in total.I’m having a few problems installing ARB on a new machine but need to start exploring this phenomenal phylogenetic resource more closely. One thing I would love when browsing large trees purely…

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…

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…

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…