Last week, an article I co-authored about the new Bio.Phylo module of Biopython was published. My primary contribution was the dedicated PAML sub-module, which eases the job of incorporating this phylogenetic analysis toolbox into computational pipelines. It is notorious for generating output which is a chore to parse, so most of the effort was involved in parsing the result files. However, the program's dependence on control files rather than commandline switches makes it a bit of a pain to script as well, so the module strives to make your life easier in that regard too.
Outside of my submodule, Bio.Phylo provides a great number of useful tools for both analyzing and visualizing phylogenetic data, and I expect the module to be of great use for many researchers.
The article was published in the open-access journal BMC Bioinformatics and you can read it here.