TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

By Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, A. von Haeseler. Bioinform., 2002

2,636 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/0c134501dc43d526d8cf22c4426efb746ac23a36

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Citations in the corpus

A molecular phylogeny of the genus Apis suggests that the Giant Honey Bee of the Philippines, A. breviligula Maa, and the Plains Honey Bee of southern India, A. indica Fabricius, are valid species (2010, methodology): “1 (Schmidt et al., 2002) was used to estimate tree topologies from the combined dataset.”
Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate (2005, methodology): “]. This alignment was then trimmed by eliminating all positions with gap characters. If the remaining length of the multiple sequence alignment was less than 100 amino acids, the entire cluster was eliminated. Phylogenetic trees were constructed by using the quartet puzzling maximum likelihood metho”
Analyses of the ribosomal internal transcribed spacers (ITS) and the 5.8s gene indicate that extremely high rDNA heterogeneity is a unique feature in the scleractinian coral genus Acropora (Scleractinia; acroporidae) (2006, methodology): “…which is distributed as X2 with (n - 2) degrees of freedom where n is the number of sequences (Felsenstein 1981, Muse and Weir 1992), was performed using TREE-PUZZLE 5.1 (Schmidt et al. 2002) to determine whether there was a statistical difference in the global evolutionary rate for 5.8S rDNA.”
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2019, methodology): “Application of the original implementation of quartet likelihood mapping in TREE-PUZZLE (Schmidt et al. 2002) (i.e., with 10,000 random quartets and exact ML quartet evaluation) to the DNA-data set took 282 min, whereas the improved implementation in IQ-TREE 2 required only 1 min using one CPU core…”
Hybridization and phylogeography of the Mozambique tilapia Oreochromis mossambicus in southern Africa evidenced by mitochondrial and microsatellite DNA genotyping (2006, methodology): “A Maximum Likelihood (ML) tree was constructed with Tree Puzzle v.5.0 using the quartet–puzzling algorithm, the Tamura and Nei (1993) substitution model and an eight-category c-distribution rate of the substitution rates across variable sites (Yang 1994) of a = 0.21, estimated from the ML approach i”
Molecular systematics of Vetigastropoda: Trochidae, Turbinidae and Trochoidea redefined (2008, methodology): “We tested the combined-gene data set using the maximum likelihood mapping method (Strimmer & von Haeseler 1997) as implemented in Tree-Puzzle (v. 5.1, Schmidt et al. 2002).”
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change (2006, methodology): “It reads trees in variants of the Newick format, including the NEXUS variant used by the package PAUP [6] and the variants used by the programs MEGA [6], PHYLIP [8], CLUS-TALX [9] and TREEPUZZLE [ 10 ].”
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 (2007, methodology): “Maximum likelihood phylogenetic analysis was performed with Tree Puzzl”
Structure is three to ten times more conserved than sequence—A study of structural response in protein cores (2009, methodology): “28 To work around an input requirement of 3 minimum sequences on input, we created input files to Tree-Puzzle in which each sequence appears in duplicate.”
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths (2009, methodology): “We used Tree-puzzle 5.2 [ 101 ] to compute the distance matrix between all strains using maximum likelihood under the HKY+gamma (with 8 categories)+I model.”
A rapid bootstrap algorithm for the RAxML Web servers. (2008, neutral): “…2005), PHYML (Guindon and Gascuel, 2003; Hordijk and Gascuel, 2005), TREEFINDER (Jobb et al., 2004), TREE-PUZZLE (Strimmer and von Haeseler, 1996; Schmidt et al., 2002), GARLI (Zwickl, 2006), DPRML (Keane et al., 2005), PHYNAV (Vinh et al., 2005), LeaPhy (Whelan, 2007), and RAxML (Stamatakis et…”
Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria (2005, methodology): “2 software and the quartet puzzling algorithm (Strimmer and vonHaeseler 1996; Schmidt et al. 2002).”
Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes) (2009, methodology): “To estimate genetic distances and phylogenetic trees among Emberiza species based on ND2 and CHD1Z, we used the software TREE-PUZZLE (Schmidt et al., 2002), which uses a maximum likelihood approach.”
DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA) 1 (2006, positive): “2 (Schmidt et al. 2002).”