New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

By Stéphane Guindon, Jean-François Dufayard, Vincent Lefort, Maria Anisimova, Wim Hordijk, Olivier Gascuel. 2010

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In Molecular Biology

Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, neutral): “This alignment was then used as an input for PAML (v.3.3.20170116) 66 to create a KaiB phylogenetic tree.”
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, methodology): “Likewise, PHYLIP output files can be directly used for Maximum Likelihood tree reconstruction analyses with RAxML [56] or PhyML [59].”
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, positive): “0 (Guindon et al., 2010) and visualized with PRESTO (http://www.”
Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. (2013, methodology): “Therefore, in addition to fast MPhy for concordant sequences, all sequences that were assigned by any of the subtyping tools as either these CRFs or the parent pure subtype (even when concordant) were also analyzed with slow MPhy (Guindon et al., 2010), which included all complete genomes of the CRF”
Zika Virus in Gabon (Central Africa) – 2007: A New Threat from Aedes albopictus? (2014, methodology): “To test for phylogenetic discrepancies, tree reconstructions were also performed independently from the envelope dataset and the NS3 dataset with PhyML according to the parameters described above.”
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets (2017, methodology): “The addition of the SPR algorithm in PhyML has significantly improved its accuracy, although at the cost of longer run-times (Guindon et al. 2010).”
Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation Schemes (2011, methodology): “Two fast implementations of ML tree search heuristics employed in this study are PHYML (Guindon and Gascuel 2003; Guindon et al. 2010) and RAxML (Stamatakis et al. 2005; Stamatakis 2006).”
How Valuable Is Financial Flexibility when Revenue Stops? Evidence from the COVID-19 Crisis (2020, neutral): “3.0 (Guindon et al.”
Title: Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice (2020, neutral): “0 (52), and a figure of this tree was made using PRESTO (http://www.”
Molecular Evolution of Human Coronavirus Genomes (2016, neutral): “, phyML [67], RaxML [68], MrBayes [69]).”