A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

By Stéphane Guindon, Olivier Gascuel. Systematic Biology, 2003

17,026 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d260b5c495daec9149319da796b9710f53deb8f3

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. (2006, methodology): “The aLRT was developed within the ML tree estimation software PHYML (Guindon and Gascuel, 2003; http://www.lirmm.fr/atgc/phyml) and an efficient implementation will be available as an option in the next release version of PHYML upon publication.”
The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, methodology): “To replicate the analysis performed with BEAST, we used the software PhyTime (from the PhyML package, Guindon 2010), which implements a Bayesian approach to estimate divergence times on a fixed tree topology.”
A rapid bootstrap algorithm for the RAxML Web servers. (2008, methodology): “…achieved over the last years in the ﬁeld of heuristic ML search algorithms with the release of programs, such as IQPNNI (Minh et al., 2005), PHYML (Guindon and Gascuel, 2003; Hordijk and Gascuel, 2005), TREEFINDER (Jobb et al., 2004), TREE-PUZZLE (Strimmer and von Haeseler, 1996; Schmidt et…”
TreeFam: 2008 Update (2007, methodology): “The species-guided PHYML allows the gene tree to have a topology that is inconsistent with the species tree if the alignment strongly supports this.”
DEFINING THE MAJOR LINEAGES OF RED ALGAE (RHODOPHYTA) 1 (2006, methodology): “4.3 (Guindon and Gascuel 2003) and unweighted maximum parsimony (MP) using PAUP*V4.”
Systematics of the Palaearctic and Oriental lizard tribe Lacertini (Squamata: Lacertidae: Lacertinae), with descriptions of eight new genera (2007, background): “of the data sets of Harris et al. (1998) and Fu (2000) shows that mitochondrial DNA provides further support for the relations indicated”
Time Tree of Rubiaceae: Phylogeny and Dating the Family, Subfamilies, and Tribes (2009, methodology): “Each chloroplast region was tested to determine the model of evolution that best fit the data by using MrAIC (Nylander 2004) with PHYML (Guindon and Gascuel 2003) and the AICc criterion (Posada and Buckley 2004).”
Distributional and demographic consequences of Pleistocene climate fluctuations for a marine demersal fish in the north‐eastern Atlantic (2009, background): “2.4.4 (Guindon & Gascuel, 2003), via a web server (Guindon et al., 2005). tcs ver.”
A new taxonomy of the family Teloschistaceae (2013, background): “0.1.1 (Guindon and Gascuel 2003, Posada 2008), evaluating only the 24 models available in MrBayes.”
Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming (2011, background): “0 (Guindon and Gascuel, 2003) with gamma and invariant sites distributions.”
Plastid phylogenomics improve phylogenetic resolution in the Lauraceae (2020, methodology): “The best‐fit DNA substitution models selected using jModelTest 2.1.10 were used for phylogeny reconstruction (Guindon & Gascuel, 2003; Darriba et al., 2012).”
Jack‐of‐all‐trades and master of many? How does associated rhizobial diversity influence the colonization success of Australian Acacia species? (2011, methodology): “The phylogenetic analysis was carried out using PhyML (Guindon & Gascuel, 2003) in Phylemon (Tárraga et al., 2007).”
Evolution and phylogeography of the tubenose goby genus Proterorhinus (Gobiidae: Teleostei): evidence for new cryptic species (2009, methodology): “…evolutionary assumptions, were used to evaluate our evolutionary hypothesis (Avise, 2004): maximum parsimony (MP) (PAUP*, version 4.0b10; Swofford, 2003), maximum likelihood (ML) (PhyML, version 2.4.4; Guindon & Gascuel, 2003), and Bayesian (MrBayes, version 3.1.2; Ronquist & Huelsenbeck, 2003).”
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix (2009, methodology): “For N = 10, we simulated 3,100 alignments (10 independent runs per family); for N = 50, we simulated 3,099 alignments; for N = 250, we simulated 308 alignments; for N = 1 , 250, we simulated only 92 alignments because some PhyML jobs did not complete, and for N = 5 , 000, we simulated 7 alignments, ”
Molecular dating of the ‘Gondwanan’ plant family Proteaceae is only partially congruent with the timing of the break‐up of Gondwana (2007, methodology): “…generates 1000 pseudo-replicates in seqboot (part of phylip version 3.63; Felsenstein, 2004), then performs a maximumlikelihood analysis in phyml (Guindon & Gascuel, 2003) for each replicate under the model of evolution selected above, and finally computes a 50% majority-rule consensus tree…”