As you might guess from the title, this course is going to be quite technical. It is probably a good idea to revise some of the calculus that you picked up a long time ago.

Semester: 2010/2011 (2)

Time: Tuesday, 5-9pm.

Venue: Bioinformatics laboratory, Block D, ISB, Faculty of Science

Important dates: Mid-term test: 22 February 2010.

Assessment mode: 60% term tests, 40% tutorials.

Course proforma: SHGS 6212 Proforma

Lectures: Week 1 ; Week 2 ; Week 3 ; Week 4 ; Week 5 ; Week 6 ; Week 7 ; Week 8 ; Week 9 ; Week 10 ; Week 11 ; Week 12 ; Week 13

Tutorials: Week 1 ; Week 2 ; Week 3 ; Week 4 ; Week 5 ; Week 6 (revised) ; Week 7 ; Week 8 ; no tutorial for Week 9 ; Week 10 ; no tutorials for Week 11 & 12; Week 13

Solutions: Tutorial 1 ; Tutorial 2 ; Tutorial 3 ; Tutorial 4 ; Tutorial 5 ; Tutorial 6 ; Tutorial 7 ; Tutorial 8

Tests: Mid-semester test ; Solution ; End of semester test

I have prepared a mathematical appendix for quick referencing. Get it here. Unfortunately, there is no short cut to learning calculus. If you have the time and inclination, you may want to follow the courseware in SHES 2303, which is basically a calculus course for bioinformatics majors.

**Errata: **

**1.** An expression for the transition probability in the Jukes-Cantor model should read: P(i|j) = 1/4[1 **–** exp(-4at) ] in Week 11’s lecture notes (page 2); in Week 12’s notes, we should have P(i|i) = 1/4[1**+**3exp(-4at)] and P(i|j) according to the preceding correction in the transition probability matrix (page 3). Apologies for the mistake and thanks to Kok Eng Piew for spotting the inconsistency.

2. See the corrected formulae for Kimura’s transition probabilities here . Thanks to Elham Kalafi and Kok Eng Piew for pointing out suspicious parts.

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## About Tsung Fei

A teacher, researcher in the bioinformatics division at the University of Malaya