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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Phylogenetic analysis and tree plotting

Phylogenetic analysis is about finding the evolutionary relationship among species (organisms), in our case, based on sequence data. Once we have a set of sequences from different sources, it becomes very interesting to understand how close or distant they are in terms of molecular evolution. As a result of the mutations during evolution, there emerge differences at the sequence level. These differences can be represented in terms of distance measures (check the See also section at the end of this recipe). These measures can then be used to estimate the evolutionary relations among the species, often represented as phylogenetic trees. This relation is very often depicted in terms of a phylogenetic tree. ...

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