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…
Category: Research
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…
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…
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…
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…
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…
Why Blog?
Why am I writing a blog? To be honest the reasons for writing change with time, but at the moment… Its theraputic. I am a big supporter of open access publishing and open source software. So extrapolating I suppose random blog-like thoughts are more beneficial out in the open than sitting on my hard drive….
EvoPhylo 