Part 6: Distance data - RAPD analysis

 

For this part you we will use the IQ-TREE.

The Random Amplified Polymorphic DNA (RAPD) assay is a method to detect genetic distances and similarity between different samples or isolates.

In this method arbitrary primers are used and polymorphic DNA is amplified from a sample. Because the primers are random, various different fragments will be amplified from the sample, and the pattern can be investigated by DNA electrophoresis.

An example of RAPD gel.

By comparing the patterns between different samples, a binary matrix can be made: the presence of a band is encoded by a 1 and the absence it is encoded by a 0.


T.foetus-KVC-1 T.foetus-LUB T.foetus-CB-1 T.foetus-UTO T.foetus-B93 T.foetus-LiL1
 
1 1 1 1 1 1
1 1 1 0 1 1
0 0 0 0 0 0
0 0 1 0 0 0
0 0 0 1 0 0
0 0 0 0 1 0
0 0 0 0 0 0
1 1 1 0 0 0
0 0 0 1 0 0
1 1 0 0 1 0

The matrix can be used further to compute distances between different samples.

Exercise 1

1. Download the file RAPD.phy and open it in a text editor.

2. Use the file to run a phylogenetic tree search using IQ-TREE.

iqtree -s INFILE -st MORPH -b 100

3. Open the resulting tree in FigTree.