Lartillot Nicolas

An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac005

2022

Article dans une revue

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Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?

Nicolas Lartillot

DOI: 10.1101/2022.04.22.489153

2022

Pré-publication

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Compositionally constrained sites drive long branch attraction

Lenard L Szantho, Nicolas Lartillot, Gergely Szöllősi, Dominik Schrempf

DOI: 10.1101/2022.03.03.482715

2022

Pré-publication

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Natural Selection beyond Life? A Workshop Report

Sylvain Charlat, André Ariew, Pierrick Bourrat, María Ferreira Ruiz, Thomas Heams, Philippe Huneman...

Life . 11 ( 10 ) : 1051

DOI: 10.3390/life11101051

2021

Article dans une revue

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Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Thibault Latrille, Nicolas Lartillot

Theoretical Population Biology . 142 : 57-66

DOI: 10.1016/j.tpb.2021.09.005

2021

Article dans une revue

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Inferring Long-Term Effective Population Size with Mutation–Selection Models

Thibault Latrille, Vincent Lanore, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 10 ) : 4573-4587

DOI: 10.1093/molbev/msab160

2021

Article dans une revue

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Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates

Mathieu Mortz, Aurore Levivier, Nicolas Lartillot, France Dufresne, Pierre Blier

Frontiers in Molecular Biosciences . 8

DOI: 10.3389/fmolb.2021.626042

2021

Article dans une revue

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Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

Emeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier

Peer Community Journal . 1 : e42

DOI: 10.24072/pcjournal.42

2021

Article dans une revue

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 3 ) : 1199-1208

DOI: 10.1093/molbev/msaa265

2021

Article dans une revue

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Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén...

Communications Biology . 4 ( 1 )

DOI: 10.1038/s42003-021-01753-7

2021

Article dans une revue

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Reconstructing the History of Variation in Effective Population Size along Phylogenies

Mathieu Brevet, Nicolas Lartillot

Genome Biology and Evolution . 13 ( 8 )

DOI: 10.1093/gbe/evab150

2021

Article dans une revue

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Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity

Dominik Schrempf, Nicolas Lartillot, Gergely Szöllősi

Molecular Biology and Evolution . 37 : 3616 - 3631

DOI: 10.1093/molbev/msaa145

2020

Article dans une revue

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Detecting sex-linked genes using genotyped individuals sampled in natural populations

Jos Käfer, Nicolas Lartillot, Gabriel Marais, Franck Picard

DOI: 10.1101/2020.01.31.928291

2020

Pré-publication

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The Bayesian Approach to Molecular Phylogeny

Nicolas Lartillot

Phylogenetics in the Genomic Era . : 1.4:1--1.4:17

2020

Chapitre d'ouvrage

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PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Nicolas Lartillot

Phylogenetics in the Genomic Era . : 1.5:1--1.5:16

2020

Chapitre d'ouvrage

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Probabilistic programming: a powerful new approach to statistical phylogenetics

Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén...

DOI: 10.1101/2020.06.16.154443

2020

Pré-publication

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Fitting diversification models on undated or partially dated trees

Nicolas Lartillot

Peer Community in Evolutionary Biology . : 100088

DOI: 10.24072/pci.evolbiol.100088

2020

Autre publication

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Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

2019

Article dans une revue

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 35 ( 11 ) : 2819-2834

DOI: 10.1093/molbev/msy173

2018

Article dans une revue

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Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

Nathanaëlle Saclier, Clémentine François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, L. Duret...

Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912

DOI: 10.1093/molbev/msy184

2018

Article dans une revue

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The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille, L. Duret, Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences .

DOI: 10.1098/rstb.2016.0463

2017

Article dans une revue

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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda, Martin Dohrmann, Walker Pett, Herve Philippe, Omar Rota-Stabelli, Nicolas Lartillot...

Current Biology - CB . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

2017

Article dans une revue

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Closing the gap between rocks and clocks using total-evidence dating

F. Ronquist, Nicolas Lartillot, M.J. Phillips

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES . 371 : 20150136

DOI: 10.1098/rstb.2015.0136

2016

Article dans une revue

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A mixed relaxed clock model

Nicolas Lartillot, M. J. Phillips, F. Ronquist

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES . 371 : 20150132

DOI: 10.1098/rstb.2015.0132

2016

Article dans une revue

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Reply to Halanych et al.

Davide Pisani, Walker Pett, Martin Dohrmann, Roberto Feuda, Omar Rota-Stabelli, Herve Philippe...

Proceedings of the National Academy of Sciences of the United States of America . 113 ( 8 ) : E948-E949

DOI: 10.1073/pnas.1525718113

2016

Article dans une revue

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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

S. Hohna, M. J. Landis, T. A. Heath, Bastien Boussau, Nicolas Lartillot, B. R. Moore...

Systematic Biology . 65 : 726-36

DOI: 10.1093/sysbio/syw021

2016

Article dans une revue

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Probabilistic models of eukaryotic evolution: time for integration

Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences . 370 ( 1678 ) : 20140338

DOI: 10.1098/rstb.2014.0338

2015

Article dans une revue

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Genomic data do not support comb jellies as the sister group to all other animals

Davide Pisani, Walker Pett, Martin Dohrmann, Roberto Feuda, Omar Rota Stabelli, Herve Philippe...

Proceedings of the National Academy of Sciences of the United States of America . 112 ( 50 ) : 15402-15407

DOI: 10.1073/pnas.1518127112

2015

Article dans une revue

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Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

N. Rodrigue, Nicolas Lartillot

Bioinformatics . 30 ( 7 ) : 1020-1

DOI: 10.1093/bioinformatics/btt729

2014

Article dans une revue

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Monte Carlo algorithms for Brownian phylogenetic models

Benjamin Horvilleur, Nicolas Lartillot

Bioinformatics . 30 ( 21 ) : 3020-3028

DOI: 10.1093/bioinformatics/btu485

2014

Article dans une revue

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Publications

An Improved Codon Modeling Approach for Accurate Estimation of the Mutation Bias

Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?

Compositionally constrained sites drive long branch attraction

Natural Selection beyond Life? A Workshop Report

Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution

Inferring Long-Term Effective Population Size with Mutation–Selection Models

Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Reconstructing the History of Variation in Effective Population Size along Phylogenies

Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity

Detecting sex-linked genes using genotyped individuals sampled in natural populations

The Bayesian Approach to Molecular Phylogeny

PhyloBayes: Bayesian Phylogenetics Using Site-heterogeneous Models

Probabilistic programming: a powerful new approach to statistical phylogenetics

Fitting diversification models on undated or partially dated trees

Detecting adaptive convergent amino acid evolution

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Closing the gap between rocks and clocks using total-evidence dating

A mixed relaxed clock model

Reply to Halanych et al.

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

Probabilistic models of eukaryotic evolution: time for integration

Genomic data do not support comb jellies as the sister group to all other animals

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

Monte Carlo algorithms for Brownian phylogenetic models