Tree-Puzzle

{{Short description|Computer program}} '''TREE-PUZZLE'''<ref name="Schmidt et al. 2002">{{cite journal | last1=Schmidt| first1=Heiko A. | last2=Strimmer | first2=Korbinian | last3=Vingron | first3=Martin | last4=von Haeseler | first4=Arndt | title=TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing | journal=Bioinformatics | volume=18 | issue=3 | date=2002 | doi=10.1093/bioinformatics/18.3.502 | pmid=11934758 | pages=502–504 | url= | pmc= | doi-access=free }}</ref> 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,<ref name="Strimmer and von Haeseler 2002">{{cite journal | last1=Strimmer | first1=Korbinian | last2=von Haeseler | first2=Arndt | title=Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment | journal=Proc. Natl. Acad. Sci. USA | volume=94 | issue=13 | date=1997 | doi=10.1073/pnas.94.13.6815 | pmid=9192648 | pages=6815–6819 | doi-access=free | url= | pmc=21241 | bibcode=1997PNAS...94.6815S }}</ref> 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 [http://www.iqtree.org/ IQ-TREE].<ref name="Nguyen et al. 2015">{{cite journal | last1=Nguyen| first1=Lam-Tung| last2=Schmidt| first2=Heiko A. | last3=von Haeseler | first3=Arndt | last4=Minh | first4=Bui Quang | title=IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies | journal=Molecular Biology and Evolution | volume=32 | issue=W1 | date=2015 | doi=10.1093/molbev/msu300 | pmid=25371430| pages=W268–W274 | url= | pmc=4271533 }}</ref>

==See also== * Computational phylogenetics

== References == {{reflist}}

==External links== * {{Official website|http://www.tree-puzzle.de}}

Category:Phylogenetics software