Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6.

Maximum-likelihood analysis using TREE-PUZZLE.

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Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Vienna, Austria.

Abstract

TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol 3 explains how to compare tree topologies using different tests.

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Maximum-likelihood analysis using TREE-PUZZLE.

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