For those of us still doing microscope counts at the microscope, I offer CellCounting, a program to help make it easier. It’s written in Perl so just run it from the command line and count your cells as usual, but reward yourself with a tab-delimited output file for all your hard work!

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 described […]