Appendix I: Required Software
The following software is required for this course, specifically the laboratory section (BIO 317L). They are all free to download and compatible for both Windows and Macintosh operating systems. If you need a loaner laptop, please see me ASAP.
Jalview
Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. We will be using it for sequence alignment and editing in lab.
Download Link: https://www.jalview.org/download/
UGENE
UGENE is a free open-source bioinformatics software for Windows, macOS and Linux. It will be especially important in lab for us to view our .abi files to check for sequence quality.
Download Link: http://ugene.net/download.html
PopART
PopART (Population Analysis with Reticulate Trees) is free population genetics software that was developed as part of the Allan Wilson Centre Imaging Evolution Initiative. We will be using it specifically to build haplotype networks in lab.
Download Link: https://popart.maths.otago.ac.nz/download/
Python
We will be using the Python programming language to perform the majority of our sequence analyses (tree construction, AMOVAs, neutrality tests, diversity analyses and data visualization). You do not need to have any experience in coding – all scripts will be provided in a “plug and play” format for you to use. In addition, we will have a crash-course on the first week of class to get you comfortable with using the command line, and understanding the bare basics of coding (language-specific syntax, code annotation, etc.).
There are several Python environments you can use to carry out your analysis. If you have never written code before, I strongly suggest THONNY which can be downloaded here. If you have taken BIO 241, then you should already have the ANACONDA platform downloaded on your laptop and you can continue to use that for this course. If you no longer have that platform, you can download it here. A video tutorial on how to install both of these platforms has been posted to this course’s Canvas site. If you run into any issues downloading and installing them on your computers, please see me during student hours.
