The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' --Isaac Asimov
That's Funny… random header image

ARB install on Kubuntu 8.10

January 26th, 2009 No Comments

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

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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 […]

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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 […]

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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: Aluminum and this forum thread: 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’ […]

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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 […]

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