| Maximum-likelihood analysis using TREE-PUZZLE (2003) | |||||||||||
Abstract | |||||||||||
| TREE-PUZZLE provides means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e. groups of 4 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.. • Unit Introduction • Basic Protocol 1: Reconstruct a Phylogenetic Tree • Basic Protocol 2: Analyze the Content of Phylogenetic Information and the Quartet Support for the Relationship of Groups of Sequences • Basic Protocol 3: Compare Tree Topologies • Support Protocol 1: Obtain and Install Tree-Puzzle for Unix/Linux and MacOS X • Support Protocol 2: Obtain and Install Tree-Puzzle for Macintosh • Support Protocol 3: Obtain and Install Tree-Puzzle for Windows • Guidelines for Understanding Results • Commentary • Bibliography Figures (thumbnail) Figures (full size) Tables | |||||||||||
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