Maximum-likelihood analysis using TREE-PUZZLE

Current Protocols in Bioinformatics
Heiko A Schmidt, A von Haeseler

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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Citations

Jul 9, 2011·Briefings in Bioinformatics·Brigitte BoeckmannChristophe Dessimoz
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Jun 2, 2012·BMC Biology·Salvador Capella-GutiérrezToni Gabaldón
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Jan 31, 2020·Journal of Medical Virology·Xingguang LiYi Li
Feb 28, 2020·Journal of Medical Virology·Xingguang LiAntoine Chaillon
Jun 21, 2016·Current Protocols in Bioinformatics·Joseph P BielawskiJoseph Mingrone
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Feb 17, 2009·Developmental Biology·Tobias LengfeldThomas W Holstein
Aug 17, 2010·Developmental Biology·Kyle A GurleyAlejandro Sánchez Alvarado

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