Hacking Trees

Parsimony is up

Stephen Smith — Mon, 04 Feb 2013 04:29:09 +0000

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

Stephen Smith — Wed, 02 Jan 2013 20:23:17 +0000

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 git tutorial here.

Python information available

Stephen Smith — Wed, 02 Jan 2013 20:18:09 +0000

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

Stephen Smith — Mon, 17 Dec 2012 14:46:33 +0000

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

blackrim — Wed, 07 Nov 2012 18:50:54 +0000

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 also recommend Practical Computing for Biologists by Haddock and Dunn. It covers topics that are in the tutorials in more depth as well as topics that are not going to be covered in the course at all (e.g., vector vs. raster figures).

Welcome

blackrim — Tue, 06 Nov 2012 18:40:55 +0000

Hacking Trees is a resource for Stephen Smith’s EEB 491 class 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.