Application of Sequence Analyses in Phylogenetic Inference

The catalog of software programs for phylogenetic analyses is available at http //evolution.gentics.washington.edu/philip/software.html. 

Phylip (Phylogenetic Inference Package) is a software package comprising about 30 command-line programs that cover almost any aspect of phylogenetic analysis 

TABLE 13.1. Phylogenetic Methods Available from Phylip 

Distance measure DnaDist DNA Compute distances to distance matrix 

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This brief guide to phylogenetic analysis has several objectives. First, a conceptual approach that describes some of the most important principles underlying the most widely and easily applied methods of phylogenetic analyses of biological sequences and their interpretation will be introduced. The aim is to show that practical phylogenetic analysis should be conceived as a search for a correct model, as much as a search for the correct tree. In this context, some of the particular models assumed by various popular methods and how these models might affect analysis of particular data sets will be discussed. Finally, some examples of the application of particular methods to the inferences of evolutionary history are provided. 

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