Topics in Systematics and Evolution: Bioinformatics for Evolutionary Biology

All of the following materials are available under the resources directory. You can follow the links in the text to find each resource.

• See the syllabus for an overview of the course.

• The Virtual Machine guide has instructions for working with VirtualBox and the Virtual Machine that will be used for all practical sessions.

• For those wanting to work on their own machine, the programs file has a listing of the software used for each exercise.

• The slides, commands, or any other information for each topic are under a directory for that topic. For example, the directory "Topic01" contains information for topic 1, the directory "Topic02" contains information for topic 2, and so on.

  • There are two directories for each topic, one for the lecture and one for the exercises.

• If you need a quick refresher (or some help getting up to speed) on working with a Unix system, take a look at the unix help file. There are some resources there that will help you find the specific command you need for each task.

• If you want to work through any of these exercises in the future or analyze your data in the cloud, create an account with DigitalOcean, install the necessary programs in the programs lists (to be updated soon!), and hack away!

All the data for each exercise will be at: www.zoology.ubc.ca/~yeaman/bioinformatics

The specific files used for each exercise will be described in the instructions provided that day.

• To access a file or directory, click that file or directory on the far left, directly over the name of the resource. If you click the message in the middle of the page, that shows what was changed in the commit, which is not what you want to look at.

The following is an up-to-date zip archive: https://github.com/UBCBio525/Bio525D/archive/master.zip

This method dosesn't require git, however, you'll have to manually update the files this way (by downloading the whole repo again).

A better method is to use git. To obtain to all the files, type:

git clone https://github.com/UBCBio525/Bio525D.git

To update the all the files at any point in the future, change to the Bio525D directory that was created by the previous command and type:

git pull

You may use any of the materials provided here, and modify them in any way, provided there is appropriate attribution according the license found below and included with this project.

Copyright (C) 2015 S. Evan Staton, Sariel Hubner, Sam Yeaman

This program is distributed under the MIT (X11) License, which should be distributed with the package. If not, it can be found here: http://www.opensource.org/licenses/mit-license.php