Distance based phylogeny reconstruction

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Distance based phylogeny reconstruction Usman Roshan

Distance-based methods

Evolutionary distances for aligned sequences We will use the Jukes Cantor model x and y are DNA/protein/RNA sequences p(x,y) is the number of mismatches in the alignment divided by the length of the alignment. This is also called the normalized Hamming distance.

Evolutionary distances for whole genomes A kmer is a substring of length k We will use an approximation to Jukes Cantor x and y are whole genome sequences This method does not require sequences to be aligned.