title: Maximum-likelihood analysis using TREE-PUZZLE.
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.
authors.affiliation: Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Vienna, Austria.
authors.forename: Heiko A
authors.initials: HA
authors.lastname: Schmidt
authors.forename: Arndt
authors.initials: A
authors.lastname: von Haeseler
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D019143:Evolution, Molecular; D016013:Likelihood Functions; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014584:User-Computer Interface