Related references
Note: Only part of the references are listed.HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models
Roberto Del Amparo et al.
GENES (2022)
Analysis of selection in protein-coding sequences accounting for common biases
Roberto Del Amparo et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Felsenstein Phylogenetic Likelihood
David Posada et al.
JOURNAL OF MOLECULAR EVOLUTION (2021)
Molecular Evolution of DNA Topoisomerase III Beta (TOP3B) in Metazoa
Filipa Moreira et al.
JOURNAL OF MOLECULAR EVOLUTION (2021)
Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics
Qiqing Tao et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability
Miguel Arenas et al.
METHODS IN ECOLOGY AND EVOLUTION (2020)
MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects
Huihui Chang et al.
BMC EVOLUTIONARY BIOLOGY (2020)
FLAVI: An Amino Acid Substitution Model for Flaviviruses
Thu Kim Le et al.
JOURNAL OF MOLECULAR EVOLUTION (2020)
Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics
Stephanie J. Spielman
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Model selection may not be a mandatory step for phylogeny reconstruction
Shiran Abadi et al.
NATURE COMMUNICATIONS (2019)
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Alexey M. Kozlov et al.
BIOINFORMATICS (2019)
The Molecular Clock in the Evolution of Protein Structures
Alberto Pascual-Garcia et al.
SYSTEMATIC BIOLOGY (2019)
The phylogenomics of evolving virus virulence
Jemma L. Geoghegan et al.
NATURE REVIEWS GENETICS (2018)
Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution
Maria Jose Jimenez-Santos et al.
PEERJ (2018)
SMS: Smart Model Selection in PhyML
Vincent Lefort et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy et al.
NATURE METHODS (2017)
Alteration of protein function by a silent polymorphism linked to tRNA abundance
Sebastian Kirchner et al.
PLOS BIOLOGY (2017)
A biologist's guide to Bayesian phylogenetic analysis
Fabricia F. Nascimento et al.
NATURE ECOLOGY & EVOLUTION (2017)
Improved mitochondrial amino acid substitution models for metazoan evolutionary studies
Vinh Sy Le et al.
BMC EVOLUTIONARY BIOLOGY (2017)
Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
Sebastian Duchene et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Influence of mutation and recombination on HIV-1 in vitro fitness recovery
Miguel Arenas et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2016)
Causes of evolutionary rate variation among protein sites
Julian Echave et al.
NATURE REVIEWS GENETICS (2016)
Selection on protein structure, interaction, and sequence
Peter B. Chi et al.
PROTEIN SCIENCE (2016)
Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life
Mikko Pentinsaari et al.
SCIENTIFIC REPORTS (2016)
Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability
Miguel Arenas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Trends in substitution models of molecular evolution
Miguel Arenas
FRONTIERS IN GENETICS (2015)
Causes, consequences and solutions of phylogenetic incongruence
Anup Som
BRIEFINGS IN BIOINFORMATICS (2015)
From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Brad R. Ruhfel et al.
BMC EVOLUTIONARY BIOLOGY (2014)
A New Formulation of Protein Evolutionary Models that Account for Structural Constraints
Andrew J. Bordner et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Pfam: the protein families database
Robert D. Finn et al.
NUCLEIC ACIDS RESEARCH (2014)
Realistic Three Dimensional Fitness Landscapes Generated by Self Organizing Maps for the Analysis of Experimental HIV-1 Evolution
Ramon Lorenzo-Redondo et al.
PLOS ONE (2014)
The Impact of Modelling Rate Heterogeneity among Sites on Phylogenetic Estimates of Intraspecific Evolutionary Rates and Timescales
Fangzhi Jia et al.
PLOS ONE (2014)
State-of the art methodologies dictate new standards for phylogenetic analysis
Maria Anisimova et al.
BMC EVOLUTIONARY BIOLOGY (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Inferring ancient divergences requires genes with strong phylogenetic signals
Leonidas Salichos et al.
NATURE (2013)
Efficient Selection of Branch-Specific Models of Sequence Evolution
Julien Y. Dutheil et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
Computer simulations: tools for population and evolutionary genetics
Sean Hoban et al.
NATURE REVIEWS GENETICS (2012)
Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model
Patrick Kueck et al.
PLOS ONE (2012)
Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
Norman R. Pace et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Is the General Time-Reversible Model Bad for Molecular Phylogenetics?
Jeremy G. Sumner et al.
SYSTEMATIC BIOLOGY (2012)
Simulation of Molecular Data under Diverse Evolutionary Scenarios
Miguel Arenas
PLOS COMPUTATIONAL BIOLOGY (2012)
phangorn: phylogenetic analysis in R
Klaus Peter Schliep
BIOINFORMATICS (2011)
ProtTest 3: fast selection of best-fit models of protein evolution
Diego Darriba et al.
BIOINFORMATICS (2011)
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
Guy Baele et al.
BMC EVOLUTIONARY BIOLOGY (2011)
Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit
Leonardo Arbiza et al.
GENOME BIOLOGY AND EVOLUTION (2011)
The importance of phylogeny to the study of phenological response to global climate change
Charles C. Davis et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2010)
Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation
Alberto Pascual-Garcia et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
Victor Soria-Carrasco et al.
BIOINFORMATICS (2007)
HIV-Specific Probabilistic Models of Protein Evolution
David C. Nickle et al.
PLOS ONE (2007)
ProtTest: selection of best-fit models of protein evolution
F Abascal et al.
BIOINFORMATICS (2005)
The importance of proper model assumption in Bayesian phylogenetics
AR Lemmon et al.
SYSTEMATIC BIOLOGY (2004)
APE: Analyses of Phylogenetics and Evolution in R language
E Paradis et al.
BIOINFORMATICS (2004)
Performance-based selection of likelihood models for phylogeny estimation
V Minin et al.
SYSTEMATIC BIOLOGY (2003)
The role of phylogenetics in comparative genetics
DE Soltis et al.
PLANT PHYSIOLOGY (2003)
Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families
D Lijavetzky et al.
BMC EVOLUTIONARY BIOLOGY (2003)
Models of protein sequence evolution and their applications
JL Thorne
CURRENT OPINION IN GENETICS & DEVELOPMENT (2000)
Share Paper
