Tree-Puzzle

TREE-PUZZLE[1] is a computer program used to construct phylogenetic trees from sequence data by maximum likelihood analysis. Branch lengths can be calculated with and without the molecular clock hypothesis.

The software also implemented likelihood mapping,[2] a method to visualize phylogenetic information in datasets, as well as several tests to assess if the likelihoods of trees are significantly worse than those of other trees.

The program's successor is IQ-TREE.[3]

See also

References
  1. Schmidt, Heiko A.; Strimmer, Korbinian; Vingron, Martin; von Haeseler, Arndt (2002). "TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing". Bioinformatics. 18 (3): 502–504. doi:10.1093/bioinformatics/18.3.502. PMID 11934758.
  2. Strimmer, Korbinian; von Haeseler, Arndt (1997). "Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment". Proc. Natl. Acad. Sci. USA. 94 (13): 6815–6819. doi:10.1073/pnas.94.13.6815. PMC 21241. PMID 9192648.
  3. Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt; Minh, Bui Quang (2015). "IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies". Molecular Biology and Evolution. 32 (W1): W268–W274. doi:10.1093/molbev/msu300. PMC 4271533. PMID 25371430.


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