Notice
5.4. The UPGMA algorithm
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Descriptif
We know how to fill an array with the values of the distances between sequences, pairs of sequences which are available in the file. This array of distances will be the input of our algorithm for reconstructing phylogenetic trees. The name of this algorithm israther complicated but the method itself is rather simple,too simple indeed. We will see that. The name standsfor Unweighted Pair Group Method with Arithmetic Mean, wewill understand these terms along the presentationof the algorithm. The algorithm starts withan array of distances. Let's take this very simpleexample, it implies seven species and here we have the values of thedistances between these different sequences associated with a species. As you remember, the array issymmetrical and all the values on the diagonal are equal to zero so here we display only the meaning ful values. So all the cells of the array are not displayed here. OK. First step consists in selectingthe smallest value of the array, this is two here which isthe distance between F and C. So since it is the smallest distance we allow to group these two species, these two nodes into a first sub tree and create a new node here which is the route of this sub tree.
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