Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion

By Derrick J. Zwickl. 2006

3,478 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f813ebf28ae4bd689a8f263b909a2f847b0fcf99

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Citations in the corpus

Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic (2012, methodology): “Trees were constructed using the maximum likelihood method in Garli 0.951 (Zwickl 2006).”
Higher-level phylogeny of the insect order Hemiptera: is Auchenorrhyncha really paraphyletic? (2011, methodology): “0 for windows (Zwickl, 2006), with each partition set to its optimal model (as described above), with these models unlinked and employing their own rates (i.”
Phylogeny of cockroaches (Insecta, Dictyoptera, Blattodea), with placement of aberrant taxa and exploration of out‐group sampling (2012, methodology): “Maximum likelihood (ML) analyses were performed in garli 1.0 (Zwickl, 2006a) on the Cipres teragrid, set to terminate after 20 000 generations without a significant change of topology.”
Developments in the taxonomy of silica-scaled chrysophytes - from morphological and ultrastructural to molecular approaches (2013, unknown): “2.0 (Zwickl 2006) and PAUP, respectively.”
New Insights into the Evolution of Passiflora subgenus Decaloba (Passifloraceae): Phylogenetic Relationships and Morphological Synapomorphies (2013, methodology): “The Q-matrices selected were all variants of TIM, TPM, TVM, or GTR. ML analyses were performed for the combined nrITS, ncpGS, ndhF, and trnL-F usingGARLI v. 2.0 (Zwickl 2006).”
Evolution in a tropical archipelago: comparative phylogeography of Philippine fauna and flora reveals complex patterns of colonization and diversification (2008, methodology): “Topologies were compared with those generated using maximum likelihood as implemented in GARLI, version 0.951 (Zwickl, 2006) in an MS-DOS environment with the most relaxed model of molecular evolution (GTR + I + G) as suggested by Kelchner & Thomas (2007).”
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. (2010, methodology): “METAPIGA (Lemmon and Milinkovitch 2002), TREEFINDER (Jobb et al. 2004), and GARLI (Zwickl 2006) use genetic algorithm–based approaches.”
Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, methodology): “0 [46] that uses a stochastic algorithm to estimate simultaneously the best topology, branch lengths and substitution model parameters that maximize the log Likelihood (lnL).”
Ancient forest fragmentation or recent radiation? Testing refugial speciation models in chameleons within an African biodiversity hotspot (2011, methodology): “Finally, a maximum likelihood (ML) search was run in garli v. 1.0 (Zwickl, 2006), using the GTR+I+G model indicated by Modeltest for the combined dataset, with all parameters estimated, and a random starting tree.”
Salvia united: The greatest good for the greatest number (2017, methodology): “Phylogenetic analyses for each LCN dataset were performed with MrBayes v.3.2.3 using the XSEDE interface of CIPRES (Miller & al., 2010) and ML using Garli v.2.0 (Zwickl, 2006).”
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics (2011, methodology): “BEAGLE is currently integrated with three state-of-the-art phylogenetic software packages: MrBayes, BEAST, and GARLI, and compatible with many more.”
Family‐level relationships of the spittlebugs and froghoppers (Hemiptera: Cicadomorpha: Cercopoidea) (2010, methodology): “Identical dataset treatments were implemented in the maximum likelihood (ML) program garli version 0.951 (Zwickl, 2006; http://www.nescent.org/informatics/download.php?software id = 4).”
Ultrafast Approximation for Phylogenetic Bootstrap (2013, methodology): “Nevertheless, as our methodology works on any set of input candidate trees, it might be worthwhile to exploit UFBoot with other tree sampling strategies such as the ge-netic algorithm (Zwickl 2006) or the Bayesian MCMC (Drummond et al. 2012; Ronquist et al. 2012).”
Citizen-science for monitoring marine invasions and stimulating public engagement: a case project from the eastern Mediterranean (2019, methodology): “Potential relationships among sequences were further examined by phylogenetic inference using Neighbour-Joining (NJ) and Maximum-Likelihood (ML) approaches generated in R (R Core Team 2013) using the ape package (Paradis et al. 2004) and the software package Garli (Zwickl 2006), respectively.”