There has been a delay (due to some traveling) in getting the multiple sequence alignment and some of the pairwise details up. However, I was able to get the parsimony up and you can see that here. The tree searching information is also getting up there over the next couple days here.
The code used throughout the site is available at bitbucket. If you aren’t familiar with git, you can either just use the download to download the code every once and a while, or you could just look at the code on the website. If you want to get more familiar with git, check out the ...
A first draft of the python tutorial and information is now available. You can find it under the tutorial section or this direct link.
I am quickly getting content into many of the sections but editing will happen later. Therefore, apologies for any bad grammar, spelling, or other typos. Despite these issues, all the code that goes up is copied directly out of scripts that are tested before copying. The code, in other words, should work fine.