Welcome 1

Hacking Trees is a resource for Stephen Smith’s EEB 491 and programming primer EEB 800 classes at University of Michigan. There are tutorials and resources for each of the subjects discussed. More information will be posted as I generate it and a guide will be placed in this posting when more material is available.

Tree manipulation and conflict analysis

Procedures to conduct analyses such as those found in https://bitbucket.org/blackrim/phyparts will be placed here. These will help folks understand how to analyze trees and compare them across genes or datasets.

New material coming!

Ramping up for a new semester teaching phylogenetics and programming. So keep an eye out for some more materials coming soon!

Programming primer

In an effort to offer a programming primer for EEB students at University of Michigan, there is an EEB 800 programming primer seminar this Winter semester. There will be more resources and exercises coming online.

Parsimony is up

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.

Code repository

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 ...

Python information available

A first draft of the python tutorial and information is now available. You can find it under the tutorial section or this direct link.

Editing apologies

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.

Computing resources for biologists

There are tutorials going up in the tutorials section for those interested. Within those you will find very basic information about each topic with links to other resources. If there are tutorials that would be useful, leaves comments or send me an email. For those interested in a general computing book for biologists, I can ...