The following example shows how easy it can be to use the three interoperability modules provided by the DendroPy Phylogenetic Computing Library to download nucleotide sequences from GenBank, align them using MUSCLE, and estimate a maximum-likelihood tree using RAxML.

The pyPDF package provides really nice facilities for PDF document manipulation. Here is a simple application script to extract a specified subset of pages from a PDF file.

It is past 4 am, and the bug hunt is over. It was a weird one. One that I'll remember. It led me on a wild exhausting chase through dark nooks and crannies of a horribly-written nightmare of a code base. What made it weird was that, with the same random number seed, I got different behavior depending on whether there were some (debugging-related) print statements in some parts of code. Even if these statements were in parts of the code that were entirely separate from where the failure was happening.

The Problem

No amount of autotools-fu could get either Python 2.4 or 2.5 satisfactory built for Mark Holder and myself on Snow Leopard. Setting a slew of environmental variables, hacking the ./configure script, the ./configure.in, or the generated Make file all yielded some manner of progress, but all ultimately ended in failure.

Here is what we initially tried and the results ...