Overview and Required Software

Over the course of the semester we will work on multiple computer tutorials to familiarize ourselves with some of the commonly used analytical tools used in molecular evolution and phylogenetics. Things to be aware of:

• Some activities will be based on your textbook, whereas others will be more computational in nature. Thus, you will likely need to download software to your computer.

• All of the programs we will use should work on both a PC and Mac. Installation instructions are provided for each system on the website for each program.

• Please make sure that you have all required software downloaded and installed before the day of the activity. Time is limited, and we do not want to spend class troubleshooting program installation.

• If you are having difficulty obtaining a program, please email your instructor so he/she can help.

• Data sets will be provided to you by your instructor.

• Below is a weekly breakdown of the programs you will need.

• Each tutorial contains questions that are intended to guide you during your analyses. Please take the time to answer each question.

• If you find that you are having difficulty answering the questions, you may need to go back to a previous topic and work more slowly.

Week 9

1. A general text editor. I recommend BBedit for Mac and Notepad++ for Windows. We will visualize and manipulate data in a text editor for several tutorials.
2. Aliview. Aliview is a general sequence alignment viewer and editor that is very user friendly.
3. SeaView. Similar to Aliview, but provides an easy way to concatenate genes into one long alignment.

Week 10

1. IQ-TREE. IQ-TREE is a program used to estimate phylogenies using the maximum likelihood (ML) criterion.
2. FigTree. FigTree is a program used to visualize phylogenetic trees (not estimate them).

Week 11

1. MrBayes. MrBayes is a program used to estimate phylogenies using Bayesian inference. It is quite versatile, and continues to be a very popular package for phylogenetic inference.
2. FigTree. FigTree is a program used to visualize phylogenetic trees (not estimate them).

Week 12

1. BEAST. Like MrBayes, BEAST is a program that can be used to estimate phylogenies using Bayesian inference. BEAST is also commonly used to infer divergence times and evolutionary rates.
2. Tracer. Tracer is a program used to monitor the results of Bayesian phylogenetic analyses. It can be used in conjunction with both BEAST and MrBayes.
3. FigTree. FigTree is a program used to visualize phylogenetic trees (not estimate them).

Week 13

1. PAUP*. PAUP* is a popular program that was originally used to estimate phylogenies using the maximum parsimony (MP) criterion. The program can also be used for ML and distance-based phylogenies. It implements the species tree method SVDquartets.
2. Aliview. Aliview is a general sequence alignment viewer and editor that is very user friendly.