Davies et al.), then you want to be able to access trees in bulk (I believe Treebase folks are working on an API though). I wrote some simple code for extracting trees from Treebase.org.Treebase is a great resource for phylogenetic trees, and has a nice interface for searching for certain types of trees. However, if you want to simply download a lot of trees for analyses (like that in
It reads an xml file of (in this case consensus) URL's for each tree, parses the xml, makes a vector of URL's, reads the nexus files with error checking, remove trees that gave errors, then a simple plot looking at metrics of the trees.
Is there an easier way to do this?