Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December. Oh, that’s not what this tip [...]
Today’s tip is going to diverge a bit from genomics today and revisit a tip I did two years ago on the Encyclopedia of Life, an ‘wiki-like’ encyclopedia of all know species. We I visited it then in the tip it was only about a year old. I had written about it a few months before [...]
Gene phylogenies (as opposed to species phylogenies) can be very useful in determined gene function, history, orthology and paralogy predictions. PhylomeDB (link added!) is a database of gene phylogenies (or as they call them, Phylomes.. no end to the ‘omes is there? . Currently there are over a dozen such phylomes from species like humans and [...]
This week’s tip of the week introduces a thesaurus of biological names, called uBio. http://www.ubio.org/ The uBio project aims to collect and organize biological names–historical and current–and make them available for searching or for use in other tools. It also contains dozens of cool links to other tools and projects around taxonomy and biodiversity around [...]
Got phylogeny? So, you’ve created a phylogeny using some software and would like to draw the tree from the Newick formatted file* you exported. Of course there is no shortage of tree drawing programs out there (or phylogeny generating ones either). We found another one recently; a web-based, API-usable, opensource tree drawing tool that is [...]
So, you’ve got your sequences aligned using Clustal, Muscle or T-Coffee (or other program), you’ve created a tree data file using PAUP, Phylip or one of the other many algorithms out there, now you want to draw and visualize those relationships. A good place to go to find a list of tools to do that [...]
Dr. Eisen at UC Davis has started a new blog theme on his “Tree of Life” blog called “Open Evolution” (open access publications, open source programs, etc) and has started with open access journals. He has listed a few open access journals (and there’s a good discussion in the comments about the difference between ‘open [...]
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