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/
ARB install on Kubuntu 8.10
January 26th, 2009 No Comments
Tags: linux · phylogeny · science
Phylogeny workflow
January 13th, 2009 No Comments
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 […]
Tags: linux · phylogeny · science
Parsimony ratchets and efficient time usage
January 6th, 2009 No Comments
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 […]
Tags: linux · phylogeny · science
kubuntu 8.10 on macbook5
November 2nd, 2008 No Comments
I just bought an aluminum macbook5,1 and successfully installed kubuntu 8.10 intrepid ibex onto it. Mostly, I used this wiki page: https://help.ubuntu.com/community/MacBook Aluminum and this forum thread: http://ubuntuforums.org/showthread.php?t=947947 UPDATE 2009-01-08: I’ve got the macbook back, now with it’s 3rd logic board and 2nd magsafe board. The tech said he thinks there was a ‘bad batch’ […]
Tags: apple · linux · open access
testing inline LaTeX
September 10th, 2008 No Comments
Using WordPress 2.6 and wp-latexrender and an installer. Success after jiggling with the paths and editing class.latexrender.php lines 197–224 to replace each instance of ‘\f’ with ‘\\f’. For example, line 203 had to be changed from $string .= "\\newsavebox{\formulabox}\n"; to $string .= "\\newsavebox{\\formulabox}\n"; This change is apparently only necessary in PHP versions >5.2.5 (thanks to […]