What is PhyloPic? PhyloPic is an awesome new service - I’ll let the creator, Mike Keesey, explain what it is (paraphrasing here): PhyloPic stores silhouette images of organisms, and each image is associated with taxonomic names, and stores the taxonomy of all taxa, allowing searching by taxonomic names. Anyone can submit silhouettes to PhyloPic. What is a silhouette? It’s like this: by Gareth Monger What makes PhyloPic not just awesome, but super awesome?...
I was just at the Phylotastic hackathon in Tucson, AZ at the iPlant facilities at the UofA. A problem that needs to be solved is getting the incrasingly vast phylogenetic information to folks not comfortable building their own phylogenies. Phylomatic has made this super easy for people that want plant phylogenies (at least 250 or so papers have used and cited Phylomatic in their papers) - however, there are few options for those that want phylogenies for other taxonomic groups....
I need to simulate balanced and unbalanced phylogenetic trees for some research I am doing. In order to do this, I do rejection sampling: simulate a tree -> measure tree shape -> reject if not balanced or unbalanced enough. But what is enough? We need to define some cutoff value to determine what will be our set of balanced and unbalanced trees. calculate shape metrics A function to calculate shape metrics, and a custom theme for plottingn phylogenies....