Practice genetics through phylogeny trees using PHYLIP software to complete the attached tutorial.
In this lab you will be guided through the process of constructing two phylogenetic trees each constructed using a different method; maximum parsimony and maximum likelihood. You will be using several programs implemented in the PHYLIP software package (http://evolution.genetics.washington.edu/phylip.html).
The PHYLogeny Inference Package (PHYLIP) is composed of 35 different programs. These programs can be divided into several different categories: phylogeny construction (including distance and maximum likelihood methods), tree drawing, editing and comparison. Detailed descriptions about the programs in each category are available (http://evolution.genetics.washington.edu/phylip/phylip.html).
PHYLIP download and installation:
Detailed instructions describing how to fetch and install the PHYLIP software package on your computer are available at the following websites (http://evolution.genetics.washington.edu/phylip/getme.html, and http://evolution.genetics.washington.edu/phylip/install.html), respectively.
This lab will focus on the use of some of these programs in order to construct a phylogeny that depicts the putative evolutionary relationship between several proteins. We will be using two different phylogeny construction programs: "protpars" (protein parsimony implementation) and "proml" (protein maximum likelihood implementation). From the Tree drawing program category we will use the "consense" and "drawgram" programs to build the consensus tree and visualize our trees, respectively.
A. Collecting Sequence Data
The construction of our phylogenetic trees requires, as an initial step, the collection and alignment of several protein sequences. We will use the myoglobin protein as our example. We will need to gather myoglobin sequences from several different species. Below are step by step instructions for collecting the data:
1.) Open a browser window and go to the NCBI website (http://www.ncbi.nlm.nih.gov/).
2.) In the Search drop down menu select "Protein" and enter "Q8T7J9" in the text box then click the Go button.
3.) Select the Q8T7J9 link to open a page providing detailed information about the specified globin. Click on the button next to the "Display Settings" link and select the FASTA radio button and then click "Apply" (see image below). The web page will refresh and display the sequence in FASTA format.
Copy this sequence to a text file.
Question 1: What is the scientific name (Genus & species) of the organism this globin protein came from?
4.) Rename the sequence in the text file by replacing the original FASTA sequence name line (i.e. everything after the > symbol) with the suggested name provided in the table 1 below.
5.) Repeat steps 2 -4 for each myoglobin/globin sequence in table 1. Add all sequences to the same text file.
Question 2: As you retrieve the sequences fill in the blanks in Table 1 with the common name of the organism in which the corresponding protein was found.
Sequence Number Protein ...
The solution practices genetics through phylogeny tree using PHYLIP software to complete a tutorial.