Volume 17, Issue 1 p. 6.6.1-6.6.23

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Maximum-Likelihood Analysis Using TREE-PUZZLE

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Heiko A. Schmidt,

Heiko A. Schmidt

Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), Vienna, Austria; University of Vienna, Austria; Medical University Vienna, Austria; University of Veterinary Medicine, Vienna, Austria

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Arndt von Haeseler,

Arndt von Haeseler

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Heiko A. Schmidt,

Heiko A. Schmidt

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Arndt von Haeseler,

Arndt von Haeseler

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First published: 01 March 2007

https://doi.org/10.1002/0471250953.bi0606s17

Citations: 29

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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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This article also appears in:

Inferring Evolutionary Relationships

Maximum-Likelihood Analysis Using TREE-PUZZLE

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