Quartet puzzling

Strimmer K., and von Haeseler, A. (1996). Quartet puzzling a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964—969. 

Figure 3 Phylogenetic relationship of the Cordyceps fungi based on the total sequence data. A tandemly concatenated nuclear and mitochondrial rDNA data set (4272 nucleotide sites) was subjected to neighbor-joining (NJ), maximum-likelihood quartet puzzling (ML-PUZZLE) and maximum parsimony (MP) analyses. The strict consensus tree of the three analyses is presented. Numbers at the nodes are bootstrap values (%) obtained by the NJ (left), ML-PUZZLE (center), and MP (right) methods, respectively. Shown on the right side are host organisms, names of the clades, and morphological types of the stromata.

Quartet puzzling is a relatively rapid tree-searching algorithm available for ML tree building (Strinuner and von Haeseler, 1996) and is available in PUZZLE. 

Robustness of the phylogenetic results was tested by bootstrap analyses (Eelsenstein 1985) (as implemented in PAUP version d65) with 100 pseudo-replications each, and quartet puzzling (QP, as implemented in PUZZLE version 4.0.1 (Strimmer and von Haeseler 1996) with 1000 puzzling steps. 

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