The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but 'That's funny...' --Isaac Asimov
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Entries from January 2009

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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