Phylogenetics in the microbiome with SuchLinkedTrees
In the last article, we saw how to use SuchTree to probe the topology of
very large trees. In this article, we're going to look at the other component
of the package, SuchLinkedTrees.
If you are interested in studying how two groups of organisms interact (or, rather, have interacted over evolutionary time), you will find yourself with two trees of distinct groups of taxa that are linked by a matrix of interaction observations. This is sometimes called a 'dueling trees' problem.
more ...SuchTree, much article
There are a lot of packages for working with and manipulating phylogenetic trees
using python. Rather than compete with packages like dendropy and ete3 on the
basis of features, SuchTree does one thing well -- its memory usage and algorithmic
complexity linearly with the number of taxa in your tree. If you need to work with
very large trees, this is very helpful.
Computing as a liberal arts degree
This is my curriculum for a liberal arts degree in technology and computing. Someone with this degree would be prepared to begin a masters degree in an engineering or technical field, but it is not intended to provide any sort of "workplace" training (although it doesn't discourage it). It would also serve as a strong base from which to purse a Ph.D. in a wide variety of topics, and would better prepare students to operate as independent researchers. In that sense, it's a liberal arts degree, not a bachelors of science.
more ...Why doesn't your lab have a 3D printer yet?
Use a 3D printer to make your own gel combes. Here's the code to design your own.
more ...