Molecular Phylogenetics
23 novembro 2015, 10:55 • Ana Teresa Correia de Freitas
The Molecular Phylogenetics homework is what will consist the evaluation of Lab V.The students are required to send a pdf with the answers to the 2 questions to jcarrico@fm.ul.pt with the subject: [BC-IST] <number of the group/day of the lab>.The code for the sequence evolution simulator should be provided through a dropbox, google drive or any other online cloud storage link, or using github. The deadline for the delivery of the report and the code is 4 December.
Some clarifications on the questions :
1) Question 1 : hamming distance vs Jukes-Cantor Correction. The starting population should be composed of a random sequence copied 100x. The hamming distance is the % of mismatching sites; there is a typo in the slides about the homework that says % of matching sites. It should read % of mismatching sites. Comment your results in face of the expected graph. If it what you expected explain it briefly, if not think of dividing the graph per areas and try to explain why it could be different of what you expect.
2) Question 2: Use the same starting population for each of the 5 scenarios