Works by Lanfear, Robert

Results: 55

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?

Published in:

PLoS Biology, 2015, v. 13, n. 10, p. 1, doi. 10.1371/journal.pbio.1002295

By:

Roche, Dominique G.;
Kruuk, Loeske E. B.;
Lanfear, Robert;
Binning, Sandra A.

Publication type:

Article

Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording.

Published in:

PLoS Biology, 2015, v. 13, n. 7, p. 1, doi. 10.1371/journal.pbio.1002190

By:

Holman, Luke;
Head, Megan L.;
Lanfear, Robert;
Jennions, Michael D.

Publication type:

Article

Troubleshooting Public Data Archiving: Suggestions to Increase Participation.

Published in:

PLoS Biology, 2014, v. 12, n. 1, p. 1, doi. 10.1371/journal.pbio.1001779

By:

Roche, Dominique G.;
Lanfear, Robert;
Binning, Sandra A.;
Haff, Tonya M.;
Schwanz, Lisa E.;
Cain, Kristal E.;
Kokko, Hanna;
Jennions, Michael D.;
Kruuk, Loeske E. B.

Publication type:

Article

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.

Published in:

PLoS Biology, 2020, v. 18, n. 12, p. 1, doi. 10.1371/journal.pbio.3000954

By:

Vanderpool, Dan;
Minh, Bui Quang;
Lanfear, Robert;
Hughes, Daniel;
Murali, Shwetha;
Harris, R. Alan;
Raveendran, Muthuswamy;
Muzny, Donna M.;
Hibbins, Mark S.;
Williamson, Robert J.;
Gibbs, Richard A.;
Worley, Kim C.;
Rogers, Jeffrey;
Hahn, Matthew W.

Publication type:

Article

The biogeographical boundaries of northern Australia: evidence from ecological niche models and a multi-locus phylogeny of Uperoleia toadlets (Anura: Myobatrachidae).

Published in:

Journal of Biogeography, 2014, v. 41, n. 4, p. 659, doi. 10.1111/jbi.12230

By:

Catullo, Renee A.;
Lanfear, Robert;
Doughty, Paul;
Keogh, J. Scott;
Kissling, W. Daniel

Publication type:

Article

Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.

Published in:

Genome Biology & Evolution, 2021, v. 13, n. 5, p. 1, doi. 10.1093/gbe/evab087

By:

Maio, Nicola De;
Walker, Conor R;
Turakhia, Yatish;
Lanfear, Robert;
Corbett-Detig, Russell;
Goldman, Nick

Publication type:

Article

sangeranalyseR: Simple and Interactive Processing of Sanger Sequencing Data in R.

Published in:

Genome Biology & Evolution, 2021, v. 13, n. 3, p. 1, doi. 10.1093/gbe/evab028

By:

Chao, Kuan-Hao;
Barton, Kirston;
Palmer, Sarah;
Lanfear, Robert

Publication type:

Article

Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants.

Published in:

Genome Biology & Evolution, 2019, v. 11, n. 12, p. 3372, doi. 10.1093/gbe/evz256

By:

Wang, Weiwen;
Lanfear, Robert

Publication type:

Article

The Prevalence and Impact of Model Violations in Phylogenetic Analysis.

Published in:

Genome Biology & Evolution, 2019, v. 11, n. 12, p. 3341, doi. 10.1093/gbe/evz193

By:

Naser-Khdour, Suha;
Minh, Bui Quang;
Zhang, Wenqi;
Stone, Eric A;
Lanfear, Robert

Publication type:

Article

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 8, p. 2319, doi. 10.1093/gbe/evw171

By:

Lanfear, Robert;
Xia Hua;
Warren, Dan L.

Publication type:

Article

Molecular Evolutionary Consequences of Island Colonization.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 6, p. 1876, doi. 10.1093/gbe/evw120

By:

James, Jennifer E.;
Lanfear, Robert;
Eyre-Walker, Adam

Publication type:

Article

Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives.

Published in:

Genome Biology & Evolution, 2014, v. 6, n. 1, p. 161, doi. 10.1093/gbe/evu005

By:

Moray, Camile;
Lanfear, Robert;
Bromham, Lindell

Publication type:

Article

Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates.

Published in:

BMC Evolutionary Biology, 2015, v. 15, n. 1, p. 1, doi. 10.1186/s12862-015-0283-7

By:

Frandsen, Paul B.;
Calcott, Brett;
Mayer, Christoph;
Lanfear, Robert

Publication type:

Article

Selecting optimal partitioning schemes for phylogenomic datasets.

Published in:

BMC Evolutionary Biology, 2014, v. 14, n. 1, p. 1, doi. 10.1186/1471-2148-14-82

By:

Lanfear, Robert;
Calcott, Brett;
Kainer, David;
Mayer, Christoph;
Stamatakis, Alexandros

Publication type:

Article

Parasitic plants have increased rates of molecular evolution across all three genomes.

Published in:

BMC Evolutionary Biology, 2013, v. 13, n. 1, p. 1, doi. 10.1186/1471-2148-13-126

By:

Bromham, Lindell;
Cowman, Peter F.;
Lanfear, Robert

Publication type:

Article

The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes.

Published in:

BMC Evolutionary Biology, 2009, v. 9, p. 1, doi. 10.1186/1471-2148-9-107

By:

Bourlat, Sarah J.;
Rota-Stabelli, Omar;
Lanfear, Robert;
Telford, Maximilian J.

Publication type:

Article

THE LOCAL-CLOCK PERMUTATION TEST: A SIMPLE TEST TO COMPARE RATES OF MOLECULAR EVOLUTION ON PHYLOGENETIC TREES.

Published in:

Evolution, 2011, v. 65, n. 2, p. 606, doi. 10.1111/j.1558-5646.2010.01160.x

By:

Lanfear, Robert

Publication type:

Article

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case.

Published in:

BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-5348-8

By:

Wang, Weiwen;
Schalamun, Miriam;
Morales-Suarez, Alejandro;
Kainer, David;
Schwessinger, Benjamin;
Lanfear, Robert

Publication type:

Article

Stability of SARS-CoV-2 phylogenies.

Published in:

PLoS Genetics, 2020, v. 16, n. 11, p. 1, doi. 10.1371/journal.pgen.1009175

By:

Turakhia, Yatish;
De Maio, Nicola;
Thornlow, Bryan;
Gozashti, Landen;
Lanfear, Robert;
Walker, Conor R.;
Hinrichs, Angie S.;
Fernandes, Jason D.;
Borges, Rui;
Slodkowicz, Greg;
Weilguny, Lukas;
Haussler, David;
Goldman, Nick;
Corbett-Detig, Russell

Publication type:

Article

MixtureFinder: Estimating DNA Mixture Models for Phylogenetic Analyses.

Published in:

Molecular Biology & Evolution, 2025, v. 42, n. 1, p. 1, doi. 10.1093/molbev/msae264

By:

Ren, Huaiyan;
Wong, Thomas K F;
Minh, Bui Quang;
Lanfear, Robert

Publication type:

Article

The Meaning and Measure of Concordance Factors in Phylogenomics.

Published in:

Molecular Biology & Evolution, 2024, v. 41, n. 11, p. 1, doi. 10.1093/molbev/msae214

By:

Lanfear, Robert;
Hahn, Matthew W

Publication type:

Article

GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models.

Published in:

Molecular Biology & Evolution, 2024, v. 41, n. 9, p. 1, doi. 10.1093/molbev/msae174

By:

Banos, Hector;
Wong, Thomas K F;
Daneau, Justin;
Susko, Edward;
Minh, Bui Quang;
Lanfear, Robert;
Brown, Matthew W;
Eme, Laura;
Roger, Andrew J

Publication type:

Article

AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era.

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 5, p. 1, doi. 10.1093/molbev/msac092

By:

Ly-Trong, Nhan;
Naser-Khdour, Suha;
Lanfear, Robert;
Minh, Bui Quang

Publication type:

Article

New Methods to Calculate Concordance Factors for Phylogenomic Datasets.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 9, p. 2727, doi. 10.1093/molbev/msaa106

By:

Minh, Bui Quang;
Hahn, Matthew W;
Lanfear, Robert

Publication type:

Article

Corrigendum to: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 8, p. 2461, doi. 10.1093/molbev/msaa131

By:

Minh, Bui Quang;
Schmidt, Heiko A;
Chernomor, Olga;
Schrempf, Dominik;
Woodhams, Michael D;
Haeseler, Arndt von;
Lanfear, Robert

Publication type:

Article

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 4, p. 1202, doi. 10.1093/molbev/msz291

By:

Duchêne, David A;
Tong, K Jun;
Foster, Charles S P;
Duchêne, Sebastián;
Lanfear, Robert;
Ho, Simon Y W

Publication type:

Article

Estimating Improved Partitioning Schemes for Ultraconserved Elements.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 7, p. 1798, doi. 10.1093/molbev/msy069

By:

Tagliacollo, Victor A;
Lanfear, Robert

Publication type:

Article

RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 4, p. 1016, doi. 10.1093/molbev/msw279

By:

Warren, Dan L.;
Geneva, Anthony J.;
Lanfear, Robert

Publication type:

Article

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 3, p. 772, doi. 10.1093/molbev/msw260

By:

Lanfear, Robert;
Frandsen, Paul B.;
Wright, April M.;
Senfeld, Tereza;
Calcott, Brett

Publication type:

Article

The Effects of Partitioning on Phylogenetic Inference.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 6, p. 1611, doi. 10.1093/molbev/msv026

By:

Kainer, David;
Lanfear, Robert

Publication type:

Article

Rapid evolution of a novel signalling mechanism by concerted duplication and divergence of a BMP ligand and its extracellular modulators.

Published in:

Development Genes & Evolution, 2010, v. 220, n. 9/10, p. 235, doi. 10.1007/s00427-010-0341-5

By:

Fritsch, Cornelia;
Lanfear, Robert;
Ray, Robert

Publication type:

Article

Body mass-corrected molecular rate for bird mitochondrial DNA.

Published in:

Molecular Ecology, 2016, v. 25, n. 18, p. 4438, doi. 10.1111/mec.13780

By:

Nabholz, Benoit;
Lanfear, Robert;
Fuchs, Jérome

Publication type:

Article

Time-dependent rates of molecular evolution.

Published in:

Molecular Ecology, 2011, v. 20, n. 15, p. 3087, doi. 10.1111/j.1365-294X.2011.05178.x

By:

HO, SIMON Y. W.;
LANFEAR, ROBERT;
BROMHAM, LINDELL;
PHILLIPS, MATTHEW J.;
SOUBRIER, JULIEN;
RODRIGO, ALLEN G.;
COOPER, ALAN

Publication type:

Article

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

Published in:

Journal of Experimental Zoology Part B: Molecular & Developmental Evolution, 2015, v. 324, n. 6, p. 517, doi. 10.1002/jez.b.22638

By:

Duchêne, Sebastian;
Lanfear, Robert

Publication type:

Article

Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora.

Published in:

Molecular Ecology Resources, 2019, v. 19, n. 1, p. 77, doi. 10.1111/1755-0998.12938

By:

Schalamun, Miriam;
Nagar, Ramawatar;
Kainer, David;
Beavan, Eleanor;
Rathjen, John P.;
Lanfear, Robert;
Schwessinger, Benjamin;
Eccles, David

Publication type:

Article

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees.

Published in:

Systematic Biology, 2024, v. 73, n. 2, p. 375, doi. 10.1093/sysbio/syae008

By:

Wong, Thomas K F;
Cherryh, Caitlin;
Rodrigo, Allen G;
Hahn, Matthew W;
Minh, Bui Quang;
Lanfear, Robert

Publication type:

Article

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.

Published in:

Systematic Biology, 2023, v. 72, n. 5, p. 1039, doi. 10.1093/sysbio/syad031

By:

Kramer, Alexander M;
Thornlow, Bryan;
Ye, Cheng;
Maio, Nicola De;
McBroome, Jakob;
Hinrichs, Angie S;
Lanfear, Robert;
Turakhia, Yatish;
Corbett-Detig, Russell

Publication type:

Article

nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Published in:

Systematic Biology, 2022, v. 71, n. 5, p. 1110, doi. 10.1093/sysbio/syac007

By:

Dang, Cuong Cao;
Minh, Bui Quang;
McShea, Hanon;
Masel, Joanna;
James, Jennifer Eleanor;
Vinh, Le Sy;
Lanfear, Robert

Publication type:

Article

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.

Published in:

Systematic Biology, 2022, v. 71, n. 4, p. 959, doi. 10.1093/sysbio/syab067

By:

Naser-Khdour, Suha;
Minh, Bui Quang;
Lanfear, Robert

Publication type:

Article

QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

Published in:

Systematic Biology, 2021, v. 70, n. 5, p. 1046, doi. 10.1093/sysbio/syab010

By:

Minh, Bui Quang;
Dang, Cuong Cao;
Vinh, Le Sy;
Lanfear, Robert

Publication type:

Article

Bayesian Estimation of Substitution Rates from Ancient DNA Sequences with Low Information Content.

Published in:

Systematic Biology, 2011, v. 60, n. 3, p. 366, doi. 10.1093/sysbio/syq099

By:

HO, SIMON Y. W.;
LANFEAR, ROBERT;
PHILLIPS, MATTHEW J.;
BARNES, IAN;
THOMAS, JESSICA A.;
KOLOKOTRONIS, SERGIOS-ORESTIS;
SHAPIRO, BETH

Publication type:

Article

Statistical Tests between Competing Hypotheses of Hox Cluster Evolution.

Published in:

Systematic Biology, 2008, v. 57, n. 5, p. 708, doi. 10.1080/10635150802430079

By:

Lanfear, Robert;
Bromham, Lindell

Publication type:

Article

Do plants have a segregated germline?

Published in:

PLoS Biology, 2018, v. 16, n. 5, p. 1, doi. 10.1371/journal.pbio.2005439

By:

Lanfear, Robert

Publication type:

Article

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses.

Published in:

Molecular Biology & Evolution, 2012, v. 29, n. 6, p. 1695, doi. 10.1093/molbev/mss020

By:

Lanfear, Robert;
Calcott, Brett;
Ho, Simon Y. W.;
Guindon, Stephane

Publication type:

Article

A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates.

Published in:

Molecular Biology & Evolution, 2010, v. 27, n. 5, p. 1173, doi. 10.1093/molbev/msq009

By:

Thomas, Jessica A.;
Welch, John J.;
Lanfear, Robert;
Bromham, Lindell

Publication type:

Article

DecentTree: scalable Neighbour-Joining for the genomic era.

Published in:

Bioinformatics, 2023, v. 39, n. 9, p. 1, doi. 10.1093/bioinformatics/btad536

By:

Wang, Weiwen;
Barbetti, James;
Wong, Thomas;
Thornlow, Bryan;
Corbett-Detig, Russ;
Turakhia, Yatish;
Lanfear, Robert;
Minh, Bui Quang

Publication type:

Article

Updated site concordance factors minimize effects of homoplasy and taxon sampling.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac741

By:

Mo, Yu K;
Lanfear, Robert;
Hahn, Matthew W;
Minh, Bui Quang

Publication type:

Article

matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2.

Published in:

Bioinformatics, 2022, v. 38, n. 15, p. 3734, doi. 10.1093/bioinformatics/btac401

By:

Ye, Cheng;
Thornlow, Bryan;
Hinrichs, Angie;
Kramer, Alexander;
Mirchandani, Cade;
Torvi, Devika;
Lanfear, Robert;
Corbett-Detig, Russell;
Turakhia, Yatish

Publication type:

Article

Broad activation of latent HIV-1 in vivo.

Published in:

Nature Communications, 2016, v. 7, n. 9, p. 12731, doi. 10.1038/ncomms12731

By:

Barton, Kirston;
Hiener, Bonnie;
Winckelmann, Anni;
Rasmussen, Thomas Aagaard;
Shao, Wei;
Byth, Karen;
Lanfear, Robert;
Solomon, Ajantha;
McMahon, James;
Harrington, Sean;
Buzon, Maria;
Lichterfeld, Mathias;
Denton, Paul W.;
Olesen, Rikke;
Østergaard, Lars;
Tolstrup, Martin;
Lewin, Sharon R.;
Søgaard, Ole Schmeltz;
Palmer, Sarah

Publication type:

Article

Taller plants have lower rates of molecular evolution.

Published in:

Nature Communications, 2013, v. 4, n. 5, p. 1879, doi. 10.1038/ncomms2836

By:

Lanfear, Robert;
Ho, Simon Y. W.;
Jonathan Davies, T.;
Moles, Angela T.;
Aarssen, Lonnie;
Swenson, Nathan G.;
Warman, Laura;
Zanne, Amy E.;
Allen, Andrew P.

Publication type:

Article