One way to assess the microbial community structure in an environment is to use a ‘fingerprinting’ technique, like T-RFLP or ARISA, to interrogate the ’species’ living there as determined from their 16S rRNA genes or some functional gene like amoA. Here’s an example of a T-RFLP electropherogram from sea ice:

You can see that most of [...]

I wrote my last paper in LaTeX and the submitted file was named ‘paper_v26′. Various other files with similar names are floating around and it is a chore to keep up with which is the latest version when they are split between two computers and three operating systems. For my thesis I decided to [...]

I added the following lines to my ‘/etc/apt/sources.list’
deb http://techno.mikro.biologie.tu-muenchen.de/debian intrepid non-free
deb http://techno.mikro.biologie.tu-muenchen.de/debian hardy non-free
and installed the packages arb (base installation), transfig (something to do with LaTeX), xfig (for exporting trees), and libmotif3 (for library libXm.so.3)
sudo apt-get install arb transfig, xfig, libmotif3
More info here: http://techno.mikro.biologie.tu-muenchen.de/

This is my general phylogeny workflow, starting with raw FASTA sequences and ending in a maximum parsimony or maximum likelihood phylogenetic tree with distances. Programs used: ARB 07.12.06org, Seaview, PAUP* 4.0 beta 10 (MacOSX), PHYLIP 3.68, ModelTest Server 1.0, PRAP2, Inkscape, XFIG.

get sequences into ARB, via e.g. greengenes or SILVA or RDP. If importing [...]

Trying to get a Parsimony (and likelihood) Ratchet protocol going I spent a couple hours trying to get PAUPRat working, including compiling an old compiler and finding old versions of libraries and editing Makefiles… then I found a newer Java program that does the same thing: PRAP2. The program includes the Likelihood ratchet protocol [...]