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 […]

Have you ever noticed hundreds of crows streaming through the shadows at dusk (probably making a ruckus)? Have you ever watched a crow chase away a bald eagle and wondered at its gumption? Have you ever been dive-bombed by a territorial crow? Have you ever wondered why? Have you ever wanted to tell someone else […]

Clearly, the publishers think there is. “[John] Conyers, a liberal Democrat whom one might expect to be on the other side of this issue, is taking harsh aim at a new National Institutes of Health (NIH) policy requiring NIH-funded scientists to archive their published papers in a publicly accessible database within a year of publication.” […]

I received a question today about monosodium glutamate (MSG), in particular the concentration of MSG in yeast and yeast extracts, which are often used as flavorings (Nutritional Yeast) and spreads (e.g. Vegemite and Marmite). As usual, I headed to the web to find the answer, and as usual in these kinds of matters, what I […]