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5.3. Building an array of distances
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So using the sequences of homologous gene between several species, our aim is to reconstruct phylogenetic tree of the corresponding species. For this, we have to comparesequences and compute distances between these sequences and we have seen last week how we were able to measure the similarity between sequences and we can use this similarity as a measureof distance between sequences. So we will compare pairs of sequences, measure the similarity and store the value of distance, of similarity into what we could call a matrix or an array. Before going further, let's makemore explicit the use of these two terms, they are not equivalentbut some people mix them. The matrix is a mathematical object,it's something you manipulate when you do linear algebra,it's a mathematical concept. An array is a computer science concept. An array is a data structure. It is true that a matrix may be implemented as an array in a program or an algorithm but notall the arrays are matrices so be careful when you use aterm matrix or its equivalent, not completely equivalent incomputer science array. So from now on we will speak of arrays because we will speak of algorithm, filling an array with the values of distances.
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