TREE-PUZZLE
is a computer program used to construct
phylogenetic tree
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...
s from sequence data by
maximum likelihood
In statistics, maximum likelihood estimation (MLE) is a method of estimation theory, estimating the Statistical parameter, parameters of an assumed probability distribution, given some observed data. This is achieved by Mathematical optimization, ...
analysis. Branch lengths can be calculated with and without the
molecular clock hypothesis
The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotid ...
.
The software also implemented likelihood mapping,
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 i
IQ-TREE
See also
*
Computational phylogenetics
References
External links
*
Phylogenetics software
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