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SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Molecular biology and evolution, 2010-02, Vol.27 (2), p.221-224

2010

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Renewing Felsenstein's phylogenetic bootstrap in the era of big data

Nature (London), 2018-04, Vol.556 (7702), p.452-456

2018

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BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Molecular biology and evolution, 1997-07, Vol.14 (7), p.685-695

Gascuel, O

1997

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Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

Nature communications, 2022-07, Vol.13 (1), p.3896-14, Article 3896

2022

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PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

Nucleic acids research, 2005-07, Vol.33 (Web Server issue), p.W557-W559

2005

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Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Nucleic acids research, 2008-07, Vol.36 (Web Server issue), p.W465-W469

2008

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Accounting for ambiguity in ancestral sequence reconstruction

Bioinformatics, 2019-11, Vol.35 (21), p.4290-4297

2019

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An Improved General Amino Acid Replacement Matrix

Molecular biology and evolution, 2008-07, Vol.25 (7), p.1307-1320

2008

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Neighbor-joining revealed

Molecular biology and evolution, 2006-11, Vol.23 (11), p.1997-2000

2006

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

Systematic biology, 2003-10, Vol.52 (5), p.696-704

2003

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On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain

Molecular biology and evolution, 1996-09, Vol.13 (7), p.999-1011

1996

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Modeling protein evolution with several amino acid replacement matrices depending on site rates

Molecular biology and evolution, 2012-10, Vol.29 (10), p.2921-2936

2012

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Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome

Parasite (Paris), 2010-12, Vol.17 (4), p.273-283

2010

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Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

IEEE/ACM transactions on computational biology and bioinformatics, 2009-01, Vol.6 (1), p.110-117

2009

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Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

Bioinformatics, 2005-12, Vol.21 (24), p.4338-4347

2005

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Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting

Molecular biology and evolution, 2004-03, Vol.21 (3), p.587-598

2004

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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Proceedings of the National Academy of Sciences - PNAS, 2020-06, Vol.117 (23), p.12522-12523

2020

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Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle

Journal of computational biology, 2002-01, Vol.9 (5), p.687-705

2002

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A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances

Molecular biology and evolution, 1994-11, Vol.11 (6), p.961-963

Gascuel, O

1994

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Topological rearrangements and local search method for tandem duplication trees

IEEE/ACM transactions on computational biology and bioinformatics, 2005-01, Vol.2 (1), p.15-28

2005

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Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Bioinformatics, 2005-09, Vol.21 (17), p.3490-3500

2005

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Hidden Markov Models with patterns to learn Boolean vector sequences and application to the built-in self-test for integrated circuits

IEEE transactions on pattern analysis and machine intelligence, 2001-09, Vol.23 (9), p.997-1008

2001

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Quartet-based phylogenetic inference: improvements and limits

Molecular biology and evolution, 2001-06, Vol.18 (6), p.1103-1116

2001

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Hidden Markov models with patterns to learn Boolean vector sequences and applications to the built-in self-test for integrated circuits

IEEE transactions on pattern analysis and machine intelligence, 2001-09, Vol.23 (9), p.997-1008

2001

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On the optimization principle in phylogenetic analysis and the minimum-evolution criterion

Molecular biology and evolution, 2000-03, Vol.17 (3), p.401-405

Gascuel, O

2000

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SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Renewing Felsenstein's phylogenetic bootstrap in the era of big data

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Accounting for ambiguity in ancestral sequence reconstruction

An Improved General Amino Acid Replacement Matrix

Neighbor-joining revealed

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain

Modeling protein evolution with several amino acid replacement matrices depending on site rates

Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome

Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood

Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle

A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances

Topological rearrangements and local search method for tandem duplication trees

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs

Hidden Markov Models with patterns to learn Boolean vector sequences and application to the built-in self-test for integrated circuits

Quartet-based phylogenetic inference: improvements and limits

Hidden Markov models with patterns to learn Boolean vector sequences and applications to the built-in self-test for integrated circuits

On the optimization principle in phylogenetic analysis and the minimum-evolution criterion

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