2. Steps of building a tree¶

2.1. Make multiple sequence alignment for Globin gene family¶

Step 1:	Download globin.fasta from Blackboard and perform a MSA using MUSCLE (follow the steps we discussed last week).
Step 2:	Examine the alignment to make sure it is correct and no additional editing is needed.
Step 2:	Export the alignment as a fasta format file on your Desktop. Name it as globin_align

Step 1:	Open the alignment file you just created by going to using Open file/Session under Data

Step 2:	Go to Explore Active Data under Data
Step 3:	Click on Pi button and this show site that are informative for Parsimony

Step 1:	Click on Phylogeny

Step 2:

Make Neighbor-Joining tree with Bootstrap 500 replicates

A:	What relationships can you see in the tree?
B:	What can you say about the statistical support for each relationship?
C:	What should be the out-group?

Step 3:

Save the tree as a pdf file by clicking on Image button

Step 4:

Build a tree using Parsimony method with 50 Bootstrap replicates (500 will be very slow).

A:	What relationships can you see in the tree?
B:	What can you say about the statistical support for each relationship?
C:	Do you see the same relationships that you saw with NJ tree?