SCC0271 - Introduction to Bioinformatics SCC-271 (2017)

Module 7: Phylogenetic Analysis

Objective

Study different phylogenetic trees from different species.

Script:

Exercise 1:

Using the mtDNA data discussed in Chapter 5, create a tree comparing human and apes. Discuss the relationship of humans with the other primates and the position of Neanderthal. Compare the trees obtained with and without the Jukes-Cantor correction.

Obs.: the mitochondrial DNA data is attached, the file is human_primates_hvr_2.fasta.

Remove the gaps and make the multiple alignment using the ClustalW, available on https://www.ebi.ac.uk/Tools/msa/clustalo/.

Exercise 2:

Get the following Genbank sequences related to HIV and SIV:

• NC_001802 - HIV­1  human
• NC_001722 - HIV­2 human
• NC_004455 - SIV mandrill (rafiki ^^)
• NC_001549 - SIV african green monkey 
• M19499 - SIV maccaca mulatta 
• M32741 - SIV pig­tailed macaque 
• X52154 - SIV chimpanzee

and build a phylogenetic tree for the HIV and SIV variations. Use the same methods from the previous exercise to build this tree.

Is it possible to identify the origins of HIV­1 and HIV­2? Analyze the generated tree.

Obs/Curiosity: Bioinformaticians usually use the Phylip tool to build phylogenetic trees.