Algoritmisk bioinformatik, algbio08Assignment 2 and corresponding synthetic data can be found below.Comment on assignment 1 problem 1. The sequences with blanks are the rows in the true alignment. This means that if X is a sequence without blanks and Y is the corresponding sequence with blanks, then the true position of position i in X is the minimal integer j such that the support of the j-prefix (i.e., the j first symbols in the sequence) of Y equals the i-prefix of X. You should measure how well you do by counting the number of positions in the sequences that are matchad with position having the same true position. New edited notes and corrected version of the second assignment:: NJ and models of sequence evolution . EM-algorithm for training HMMs . File with synthetic data generated from the model in assignment 2. Contains 10000 samples with m=n=6 .
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