Stephane Guindon

49
Documents
Current affiliation
  • Méthodes et Algorithmes pour la Bioinformatique (LIRMM | MAB)

Presentation

I design probabilistic models of evolution and algorithms to infer their parameters from the analysis of molecular, fossil and/or spatial data. I created and am still developping the software package [PhyML](https://github.com/stephaneguindon/phyml) (for Phylogenetics through Maximum Likelihood) which serves as a basis to implement my research outputs.
Trained as a biologist/statistician, I am working as a CNRS research scientist in the computer science department of the [LIRMM](https://www.lirmm.fr/equipes/MAB/) in Montpellier, France. I was also lucky to work for the [Department of Statistics](https://www.auckland.ac.nz/en/science/about-the-faculty/department-of-statistics.html) at the University of Auckland between 2007 and 2015.

Miscellaneous

Associate editor for Systematic Biology and BMC Evolutionary Biology. Scientific head of the ATGC platform. Co-chair and organizer of the annual conference "Mathematical and Computational Evolution". Served as member of the council for the Society of Systematic Biologists (until 2016). PI on ANR grant GENOSPACE (2016-2021) and Royal Society of New Zealand Marsden grant (2008-2011)

Research domain

Bioinformatics [q-bio.QM]

Publications

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Publications

Image document

Modeling the velocity of evolving lineages and predicting dispersal patterns

Paul Bastide , Pauline Rocu , Johannes Wirtz , Gabriel Hassler , François Chevenet et al.
Proceedings of the National Academy of Sciences of the United States of America, 2024, 121 (47), pp.e2411582121. ⟨10.1073/pnas.2411582121⟩
Journal articles (Review article) lirmm-04795029 v1

On the connections between the spatial Lambda–Fleming–Viot model and other processes for analysing geo-referenced genetic data

Johannes Wirtz , Stéphane Guindon
Theoretical Population Biology, 2024, 158, pp.139-149. ⟨10.1016/j.tpb.2024.06.002⟩
Journal articles hal-04795059 v1
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How fast are viruses spreading in the wild?

Simon Dellicour , Paul Bastide , Pauline Rocu , Denis Fargette , Olivier Hardy et al.
PLoS Biology, 2024, 22 (12), pp.e3002914. ⟨10.1371/journal.pbio.3002914⟩
Journal articles hal-04874886 v1
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EvoLaps 2 : Advanced phylogeographic visualization

François Chevenet , Denis Fargette , Paul Bastide , Thomas Vitré , Stéphane Guindon
Virus Evolution, 2024, 10 (1), pp.1-9. ⟨10.1093/ve/vead078⟩
Journal articles hal-04531387 v1
Image document

Rate of coalescence of lineage pairs in the Spatial Λ -Fleming–Viot process

Johannes Wirtz , Stéphane Guindon
Theoretical Population Biology, 2022, 146, pp.15-28. ⟨10.1016/j.tpb.2022.05.002⟩
Journal articles lirmm-03875375 v1
Image document

Éclairer les origines de la COVID-19 à partir de l’analyse comparée des génomes viraux

Stéphane Guindon , Celine Scornavacca
Interstices, 2022
Journal articles hal-03872208 v1
Image document

EvoLaps: a web interface to visualize continuous phylogeographic reconstructions

François Chevenet , Denis Fargette , Stéphane Guindon , Anne-Laure Bañuls
BMC Bioinformatics, 2021, 22 (1), pp.#463. ⟨10.1186/s12859-021-04386-z⟩
Journal articles hal-03378825 v1
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Accounting for spatial sampling patterns in Bayesian phylogeography

Stéphane Guindon , Nicola de Maio
Proceedings of the National Academy of Sciences of the United States of America, 2021, 118 (52), pp.e2105273118. ⟨10.1073/pnas.2105273118⟩
Journal articles lirmm-03875373 v1
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Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley

Souley Issaka , Oumar Issiaka I. Traore , Régis Dimitri Skopé Longué , Agnès Pinel-Galzi , Mandev S. Gill et al.
Virus Evolution, 2021, 7 (2), pp.veab072. ⟨10.1093/ve/veab072⟩
Journal articles hal-03365735 v1
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Sampling bias and model choice in continuous phylogeography: getting lost on a random walk

Antanas Kalkauskas , Umberto Perron , Yuxuan Sun , Nick Goldman , Guy Baele et al.
PLoS Computational Biology, 2021, 17 (1), pp.e1008561. ⟨10.1371/journal.pcbi.1008561⟩
Journal articles hal-03064800 v2
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Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

Stéphane Guindon
Frontiers in Genetics, 2020, 11, pp.#526. ⟨10.3389/fgene.2020.00526⟩
Journal articles lirmm-03064771 v1
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Accounting for ambiguity in ancestral sequence reconstruction

Adrien Oliva , Sylvain Pulicani , Vincent Lefort , Laurent Brehelin , Olivier Gascuel et al.
Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩
Journal articles pasteur-02404399 v1
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Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a “Doubly Intractable” Problem

Stéphane Guindon
Systematic Biology, 2018, 67 (4), pp.651-661. ⟨10.1093/sysbio/syy003⟩
Journal articles lirmm-01800299 v1
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HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences

Oliver Ratmann , Chris Wymant , Caroline Colijn , Siva Danaviah , Max Essex et al.
AIDS Research and Human Retroviruses, 2017, 33 (11), pp.1083-1098. ⟨10.1089/aid.2017.0061⟩
Journal articles lirmm-01800302 v1

Demographic inference under the coalescent in a spatial continuum

Stéphane Guindon , Hongbin Guo , David Welch
Theoretical Population Biology, 2016, 111, pp.43-50. ⟨10.1016/j.tpb.2016.05.002⟩
Journal articles lirmm-01347481 v1

Closed form modeling of evolutionary rates by exponential Brownian functionals

Nicolas Privault , Stéphane Guindon
Journal of Mathematical Biology, 2015, 71 (6), pp.1387-1409. ⟨10.1007/s00285-015-0863-6⟩
Journal articles lirmm-01233099 v1
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Molecular Evolution of the TET Gene Family in Mammals

Hiromichi Akahori , Stéphane Guindon , Sumio Yoshizaki , Yoshinori Muto
International Journal of Molecular Sciences, 2015, 16 (12), pp.28472-28485. ⟨10.3390/ijms161226110⟩
Journal articles lirmm-01286570 v1

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

Tanja Stadler , Timothy G. Vaughan , Alex Gavryushkin , Stéphane Guindon , Denise Kühnert et al.
Proceedings of the Royal Society B: Biological Sciences, 2015, 282 (1806), pp.20150420. ⟨10.1098/rspb.2015.0420⟩
Journal articles lirmm-01349044 v1
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Modelling Competition and Dispersal in a Statistical Phylogeographic Framework

Louis Ranjard , David Welch , Marie Paturel , Stéphane Guindon
Systematic Biology, 2014, 63 (5), pp.743-752. ⟨10.1093/sysbio/syu040⟩
Journal articles lirmm-01233106 v1
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From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages

Stéphane Guindon
Systematic Biology, 2013, 62 (1), pp.22-34. ⟨10.1093/sysbio/sys063⟩
Journal articles lirmm-00805052 v1

Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion

Stéphane Guindon , Yan Cheng , Allen Rodrigo , Lin Wing Wee , Inoue Masafumi et al.
Gut, 2012, 62 (9), pp.1347-1355. ⟨10.1136/gutjnl-2012-302408⟩
Journal articles istex lirmm-00805051 v1
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PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Stéphane Guindon , Robert Lanfear , Brett Calcott , Simon Y.W. Ho
Molecular Biology and Evolution, 2012, 29 (6), pp.1695-1701. ⟨10.1093/molbev/mss020⟩
Journal articles lirmm-00705211 v1
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The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

Julien Soubrier , Mike Steel , Michael S.Y. Lee , Clio Der Sarkissian , Stéphane Guindon et al.
Molecular Biology and Evolution, 2012, 29 (11), pp.3345-3358. ⟨10.1093/molbev/mss140⟩
Journal articles lirmm-00805053 v1
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Bayesian Estimation of Divergence Times From Large Sequence Alignments

Stéphane Guindon
Molecular Biology and Evolution, 2010, 27 (8), pp.1768-1781. ⟨10.1093/molbev/msq060⟩
Journal articles lirmm-00705189 v1
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SeaView Version 4: a Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

Manolo Gouy , Stéphane Guindon , Olivier Gascuel
Molecular Biology and Evolution, 2010, 27, pp.221-224. ⟨10.1093/molbev/msp259⟩
Journal articles lirmm-00511794 v2
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New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Stéphane Guindon , Jean-François Dufayard , Vincent Lefort , Maria Anisimova , Wim Hordijk et al.
Systematic Biology, 2010, 59 (3), pp.307-321. ⟨10.1093/sysbio/syq010⟩
Journal articles lirmm-00511784 v2
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist

Alexis Dereeper , Valentin Guignon , Guillaume Blanc , Stéphane Audic , Sylvain Buffet et al.
Nucleic Acids Research, 2008, 36 (Web Server), pp.W465-W469. ⟨10.1093/nar/gkn180⟩
Journal articles lirmm-00324099 v1
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Genomics, biogeography, and the diversification of placental mammals

Derek E. Wildman , Monica Uddin , Juan C. Opazo , Guozhen Liu , Vincent Lefort et al.
Proceedings of the National Academy of Sciences of the United States of America, 2007, 104 (36), pp.14395-14400. ⟨10.1073/pnas.0704342104⟩
Journal articles lirmm-00193171 v1
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Identification of NF-kappaB Responsive Elements in Follistatin Related Gene (FLRG) Promoter

Laurent Bartholin , Stéphane Guindon , Sylvie Martel , Laura Corbo , Ruth Rimokh
Gene, 2007, 393, pp.153-162. ⟨10.1016/j.gene.2007.02.007⟩
Journal articles lirmm-00171207 v2
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Control of the False Discovery Rate Applied to the Detection of Positively Selected Amino Acid Sites

Stéphane Guindon , Mik Black , Allen Rodrigo
Molecular Biology and Evolution, 2006, 23 (5), pp.919-926. ⟨10.1093/molbev/msj095⟩
Journal articles lirmm-00135171 v1
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PHYML Online: A Web Server for Fast Maximum Likelihood-Based Phylogenetic Inference

Stéphane Guindon , F. Le Thiec , Patrice Duroux , Olivier Gascuel
Nucleic Acids Research, 2005, 33, pp.557-559. ⟨10.1093/nar/gki352⟩
Journal articles lirmm-00105317 v1

Modeling the Site-Specific Variation of Selection Patterns Along Lineages

Stéphane Guindon , Allen Rodrigo , Kelly Dyer , John Huelsenbeck
Proceedings of the National Academy of Sciences of the United States of America, 2004, 101, pp.12957-12962. ⟨10.1073/pnas.0402177101⟩
Journal articles lirmm-00171208 v1
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A Simple, Fast, and Accurate Method to Estimate Large Phylogenies by Maximum Likelihood

Stéphane Guindon , Olivier Gascuel
Systematic Biology, 2003, 52 (5), pp.696-704. ⟨10.1080/10635150390235520⟩
Journal articles lirmm-00191949 v1
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Efficient Based Estimation of Evolutionary Distance when Substitution Rates Vary Across Sites

Stéphane Guindon , Olivier Gascuel
Molecular Biology and Evolution, 2002, 19 (4), pp.534-543. ⟨10.1093/oxfordjournals.molbev.a004109⟩
Journal articles lirmm-00268454 v1
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Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes

Stéphane Guindon , G. Perrière
Molecular Biology and Evolution, 2001, 18 (9), pp.1838-1840. ⟨10.1093/oxfordjournals.molbev.a003972⟩
Journal articles hal-00427178 v1

Trees: Combinatorics and Models

Gilles Didier , Stéphane Guindon
Models and Methods for Biological Evolution: Mathematical Models and Algorithms to Study Evolution, Chapter 1, Wiley, pp.1-26, 2024, 9781789450699. ⟨10.1002/9781394284252.ch1⟩
Book sections lirmm-04824198 v1
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Arbres : combinatoire et modèles

Gilles Didier , Stéphane Guindon
Modèles et méthodes pour l’évolution biologique, iSTE Edition, pp.7-32, 2022, 9781789480696. ⟨10.51926/ISTE.9069.ch1⟩
Book sections hal-03485566 v1

Numerical Optimization Techniques in Maximum Likelihood Tree Inference

Stéphane Guindon , Olivier Gascuel
Tandy Warnow. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, 29, Springer, pp.21-38, 2019, Computational Biology (COBO), 978-3-030-10837-3. ⟨10.1007/978-3-030-10837-3_2⟩
Book sections pasteur-02405302 v1
Image document

Estimating maximum likelihood phylogenies with PhyML

Stéphane Guindon , Frédéric Delsuc , Jean-François Dufayard , Olivier Gascuel
David Posada. Bioinformatics for DNA Sequence Analysis, 537, Springer Protocols, pp.113-137, 2009, Methods in Molecular Biology, ⟨10.1007/978-1-59745-251-9_6⟩
Book sections lirmm-00511830 v1

Modelling the Variability of Evolutionary Processes

Olivier Gascuel , Stéphane Guindon
Olivier Gascuel; M. Steel. Reconstructing Evolution: New Mathematical and Computational Advances, II Models of sequence evolution, pp.65-99, 2007, 0199208220
Book sections lirmm-00171206 v1

Models and Methods for Biological Evolution

Gilles Didier , Stéphane Guindon
Anne Siegel; Hélène Touzet. ISTE - WILEY, pp.1-307, 2024, Models and Methods for Biological Evolution, 9781789450699. ⟨10.1002/9781394284252⟩
Books hal-04795193 v1

Modèles et méthodes pour l’évolution biologique

Gilles Didier , Stéphane Guindon
iSTE Edition, 330 p., 2022, 9781789480696
Books lirmm-03766511 v1
Image document

Méthodes et algorithmes pour l'approche statistique en phylogénie

Stéphane Guindon
Bio-Informatique, Biologie Systémique [q-bio.QM]. Université Montpellier II - Sciences et Techniques du Languedoc, 2003. Français. ⟨NNT : ⟩
Theses tel-00843343 v1