Estimating maximum likelihood phylogenies with PhyML.

By Stéphane Guindon, Frédéric Delsuc, Jean-François Dufayard, Olivier Gascuel. Methods in molecular biology, 2009

816 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/13134f338f0de883336e34039db9376f85a78a99

How researchers see this paper

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

In Genetics

1. Erfan Sayyari
2. Siavash Mirarab
3. J. Neuhaus
4. Morgan N. Price
5. Adam P. Arkin
6. Y. Van de Peer
7. Paramvir S. Dehal
8. Robert C. Edgar

In Molecular Biology

1. Erfan Sayyari
2. Siavash Mirarab
3. Morgan N. Price
4. Adam P. Arkin
5. Paramvir S. Dehal
6. P. Ozias‐Akins
7. Y. Chu
8. Y. Van de Peer

In Paleontology

1. Morgan N. Price
2. Adam P. Arkin
3. Siavash Mirarab
4. Erfan Sayyari
5. Y. Van de Peer
6. Paramvir S. Dehal

Citations in the corpus

• The Evolution and Emergence of RNA Viruses (2009, neutral): “[66]), excluding poorly aligned regions.”
• PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017, methodology): “Finally, the phylogenetic tree construction method has to be defined, which can be either the approximate maximum likelihood method FastTree, or the maximum likelihood methods PhyML (21), RaXML (22) or IQ-TREE (23).”
• Recombination is suppressed in an alien introgression in peanut harboring Rma, a dominant root-knot nematode resistance gene (2010, methodology): “NBS sequences were phylogenetically classified by maximum-likelihood (ML) methods and PHYML (Guindon et al. 2005, 2009).”
• Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis (2019, methodology): “mitis and 25 representative Streptococcus pneumoniae strains (with Streptococcus pyogenes as an outgroup) with the patient’s 16S rRNA sequence with the use of MAFFT(20) at default settings, followed by tree construction with the use of PhyML.(21) Panel E shows analysis of antibiotic-resistance genes”
• FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010, methodology): “We will show that in practice, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs, PhyML 3 with default settings [16,17].”
• Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies (2016, methodology): “Similar assumptions have been made in past for fast calculation of local support in the context of maximum likelihood (ML) tree reconstruction from sequence data; for example, aLRT in PhyML (Guindon et al. 2009) and SH-like support in FastTree-II (Price et al.”