Wiki source code of Methods, distance-based

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1 The data used as a basis for phylogenetic inference commonly arises from gene sequencing procedures or by performing a number of phenotypic measurements. However, the way the data is used varies from method to method. In distance-based methods, the data is first transformed into a [[distance matrix>>doc:stemmatology.Distance matrix.WebHome]] that gives, for each pair of [[taxa>>doc:stemmatology.Taxon.WebHome]], a pairwise distance. The distance can be, for instance, the number of characters that differ between the two taxa divided by the length of the sequences. (Note that in case a specific sequence evolution model, such as the common Jukes-Cantor model is used, it may be beneficial to carry out a correction based on the model.)
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3 Once a distance matrix is computed, a distance-based method ignores the original data and bases its operation only on the distance matrix. A popular distance-based method is the [[neighbour joining>>doc:stemmatology.Neighbour joining.WebHome]] method. An example of a method that is //not// distance-based is the [[maximum parsimony>>doc:stemmatology.Method, maximum parsimony.WebHome]] method.
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5 ==== **Reference** ====
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7 – Lemey, Philippe, Marco Salemi, and Anne-Mieke Vandamme, eds. 2009. //The// //Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing.// 2nd ed. Cambridge: Cambridge University Press.
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9 **In other languages**
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11 DE: distanzbasierte Methoden
12 FR: méthodes basées sur les distances
13 IT: metodi basati sulla distanza
14 \\[[TR>>doc:stemmatology.Parvum lexicon stemmatologicum.Contributors.WebHome]]