assignment-5

assignment-5 - BSC5936-Fall 2005 Computational Evolutionary...

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BSC5936-Fall 2005 Computational Evolutionary Biology Assignment 5 – Simulation of data on trees We will learn in this assignment to generate data on a pre-specified tree. This method is used for many situations, such as testing computer programs, parametric bootstrapping, and very recently also for approximative Bayes methods (Majoram et al. 2004, Beaumont 2004) [citations needs checking]. The general principle for simulating data follows simple rules. 1. We need a mutation model, for example the Hasegawa-Kishino-Jano model and specify the transition rate matrix: Q = - μ ( π C + κπ G + π T ) μπ C κμπ G μπ T μπ A - μ ( π A + π G + κπ T ) μπ G κμπ T κμπ A μπ C - μ ( κπ A + π C + π T ) μπ T μπ A κμπ C μπ G - μ ( π A + κπ C + π G ) 2. Start at the root of the tree with an arbitrary nucleotide, for example picked at random from the { A,C,G,T } . 3. The rate matrix tells us what are the possible rates of change starting with this arbitrary
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assignment-5 - BSC5936-Fall 2005 Computational Evolutionary...

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