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Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences

https://doi.org/10.1093/molbev/msj021
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471650129.dob0522openalex-snapshot
PAUP * [Phylogenetic Analysis Using Parsimony (and Other Methods)]
inferredcites →https://doi.org/10.1007/bf00160154openalex-snapshot
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
inferredcites →https://doi.org/10.1007/bf00166252openalex-snapshot
Statistical tests of models of DNA substitution
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
inferredcites →https://doi.org/10.1007/bf02101990openalex-snapshot
A new method for calculating evolutionary substitution rates
inferredcites →https://doi.org/10.1007/bf02352289openalex-snapshot
Maximum-likelihood models for combined analyses of multiple sequence data
inferredcites →https://doi.org/10.1007/s002390010173openalex-snapshot
The Effect of Branch Length Variation on the Selection of Models of Molecular Evolution
inferredcites →https://doi.org/10.1038/nature02053openalex-snapshot
Genome-scale approaches to resolving incongruence in molecular phylogenies
inferredcites →https://doi.org/10.1080/10635150119297openalex-snapshot
The Troubled Growth of Statistical Phylogenetics
inferredcites →https://doi.org/10.1080/10635150490522304openalex-snapshot
Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/14.9.817openalex-snapshot
MODELTEST: testing the model of DNA substitution.
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/genetics/155.1.431openalex-snapshot
Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
inferredcites →https://doi.org/10.1093/oso/9780198548249.003.0012openalex-snapshot
The role of models in reconstructing evolutionary trees
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004094openalex-snapshot
The Effects of Nucleotide Substitution Model Assumptions on Estimates of Nonparametric Bootstrap Support
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025811openalex-snapshot
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026137openalex-snapshot
Topological bias and inconsistency of maximum likelihood using wrong models
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040152openalex-snapshot
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.

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inferred← citeshttps://doi.org/10.1016/j.ympev.2009.09.035openalex-snapshot
Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta)
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.01.038openalex-snapshot
Molecular systematics and evolutionary biogeography of the genus Talpa (Soricomorpha: Talpidae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.02.003openalex-snapshot
Phylogeography of endemic toads and post-Pliocene persistence of the Brazilian Atlantic Forest
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.02.007openalex-snapshot
Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.04.039openalex-snapshot
Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.06.018openalex-snapshot
Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data
inferred← citeshttps://doi.org/10.1016/j.ympev.2010.08.010openalex-snapshot
Phylogenetics of the pademelons (Macropodidae: Thylogale) and historical biogeography of the Australo-Papuan region
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.04.004openalex-snapshot
Species tree of a recent radiation: The subfamily Delphininae (Cetacea, Mammalia)
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.11.021openalex-snapshot
Phylogenetic analyses reveal extensive cryptic speciation and host specialization in an economically important mite taxon
inferred← citeshttps://doi.org/10.1016/j.ympev.2012.12.003openalex-snapshot
Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.03.027openalex-snapshot
New molecular phylogeny of the squids of the family Loliginidae with emphasis on the genus Doryteuthis Naef, 1912: Mitochondrial and nuclear sequences indicate the presence of cryptic species in the southern Atlantic Ocean
inferred← citeshttps://doi.org/10.1016/j.ympev.2013.08.003openalex-snapshot
Historical biogeography of Eastern Asian–Eastern North American disjunct Melaphidina aphids (Hemiptera: Aphididae: Eriosomatinae) on Rhus hosts (Anacardiaceae)
inferred← citeshttps://doi.org/10.1016/j.ympev.2014.04.010openalex-snapshot
Using multiple relaxed-clock models to estimate evolutionary timescales from DNA sequence data
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.06.005openalex-snapshot
A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
inferred← citeshttps://doi.org/10.1016/j.ympev.2015.09.002openalex-snapshot
Phylogenetic relationships and evolutionary history of the Mesoamerican endemic freshwater fish family Profundulidae (Cyprinodontiformes: Actinopterygii)
inferred← citeshttps://doi.org/10.1016/j.ympev.2017.05.026openalex-snapshot
Correlated evolutionary rates across genomic compartments in Annonaceae
inferred← citeshttps://doi.org/10.1016/j.ympev.2019.106617openalex-snapshot
Evolutionary dynamics of lineage 2 West Nile virus in Europe, 2004–2018: Phylogeny, selection pressure and phylogeography
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.107001openalex-snapshot
Unraveling elephant-shrews: Phylogenetic relationships and unexpected introgression among giant sengis
inferred← citeshttps://doi.org/10.1016/s2352-3018(18)30062-6openalex-snapshot
Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data
inferred← citeshttps://doi.org/10.1017/cbo9781139095112openalex-snapshot
Bayesian Evolutionary Analysis with BEAST
inferred← citeshttps://doi.org/10.1017/s0950268825000251openalex-snapshot
The evolution and epidemiology of H3N2 canine influenza virus after 20 years in dogs
inferred← citeshttps://doi.org/10.1038/ismej.2011.93openalex-snapshot
Phylodynamics and movement of Phycodnaviruses among aquatic environments
inferred← citeshttps://doi.org/10.1038/ismej.2015.178openalex-snapshot
Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies
inferred← citeshttps://doi.org/10.1038/nature06945openalex-snapshot
The genomic and epidemiological dynamics of human influenza A virus
inferred← citeshttps://doi.org/10.1038/nature12515openalex-snapshot
The genesis and source of the H7N9 influenza viruses causing human infections in China
inferred← citeshttps://doi.org/10.1038/nature13016openalex-snapshot
A synchronized global sweep of the internal genes of modern avian influenza virus
inferred← citeshttps://doi.org/10.1038/nature14348openalex-snapshot
Dissemination, divergence and establishment of H7N9 influenza viruses in China
inferred← citeshttps://doi.org/10.1038/nature14460openalex-snapshot
Global circulation patterns of seasonal influenza viruses vary with antigenic drift
inferred← citeshttps://doi.org/10.1038/nature22400openalex-snapshot
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
inferred← citeshttps://doi.org/10.1038/nature22401openalex-snapshot
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
inferred← citeshttps://doi.org/10.1038/nature22402openalex-snapshot
Zika virus evolution and spread in the Americas
inferred← citeshttps://doi.org/10.1038/ncomms8952openalex-snapshot
Phylodynamics of H1N1/2009 influenza reveals the transition from host adaptation to immune-driven selection
inferred← citeshttps://doi.org/10.1038/nrg3186openalex-snapshot
Molecular phylogenetics: principles and practice
inferred← citeshttps://doi.org/10.1038/s41426-018-0185-zopenalex-snapshot
Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis
inferred← citeshttps://doi.org/10.1038/s41426-018-0190-2openalex-snapshot
Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006–2016)
inferred← citeshttps://doi.org/10.1038/s41467-019-13287-yopenalex-snapshot
Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza
inferred← citeshttps://doi.org/10.1038/s41467-020-16567-0openalex-snapshot
Vulnerabilities in coronavirus glycan shields despite extensive glycosylation
inferred← citeshttps://doi.org/10.1038/s41467-024-45462-1openalex-snapshot
Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders
inferred← citeshttps://doi.org/10.1038/s41467-024-51490-8openalex-snapshot
Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region
inferred← citeshttps://doi.org/10.1038/s41467-025-55840-yopenalex-snapshot
Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia
inferred← citeshttps://doi.org/10.1038/s41559-017-0280-xopenalex-snapshot
A biologist’s guide to Bayesian phylogenetic analysis
inferred← citeshttps://doi.org/10.1038/s41564-024-01732-8openalex-snapshot
Immune imprinting in early life shapes cross-reactivity to influenza B virus haemagglutinin
inferred← citeshttps://doi.org/10.1038/s41564-025-02254-7openalex-snapshot
Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats
inferred← citeshttps://doi.org/10.1038/s41586-025-09737-xopenalex-snapshot
Ecology and spread of the North American H5N1 epizootic
inferred← citeshttps://doi.org/10.1038/s41586-026-10394-xopenalex-snapshot
Heart-nosed bat alphacoronaviruses use human CEACAM6 to enter cells
inferred← citeshttps://doi.org/10.1038/s41598-017-10605-6openalex-snapshot
First genome report and analysis of chicken H7N9 influenza viruses with poly-basic amino acids insertion in the hemagglutinin cleavage site
inferred← citeshttps://doi.org/10.1038/s41598-018-23913-2openalex-snapshot
Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak
inferred← citeshttps://doi.org/10.1038/s41598-018-30528-0openalex-snapshot
Epidemic history of hepatitis C virus genotypes and subtypes in Portugal
inferred← citeshttps://doi.org/10.1038/s41598-018-37458-xopenalex-snapshot
Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations
inferred← citeshttps://doi.org/10.1038/s41598-019-41995-4openalex-snapshot
The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa
inferred← citeshttps://doi.org/10.1038/s41598-019-47209-1openalex-snapshot
Phylogeographic and genetic characterization of porcine circovirus type 2 in Taiwan from 2001–2017
inferred← citeshttps://doi.org/10.1038/s41598-019-53422-9openalex-snapshot
Evidence of CPV2c introgression into Croatia and novel insights into phylogeny and cell tropism
inferred← citeshttps://doi.org/10.1038/s41598-020-59944-xopenalex-snapshot
Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread
inferred← citeshttps://doi.org/10.1038/s41598-020-62547-1openalex-snapshot
Architectural evolution in cocoons spun by Hyalophora (Lepidoptera; Saturniidae) silk moth species
inferred← citeshttps://doi.org/10.1038/s41598-020-69692-7openalex-snapshot
Epidemic history and baseline resistance to NS5A-specific direct acting drugs of hepatitis C virus in Spain
inferred← citeshttps://doi.org/10.1038/s41598-021-84583-1openalex-snapshot
Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes
inferred← citeshttps://doi.org/10.1038/s41598-021-90023-xopenalex-snapshot
Identification of CRF89_BF, a new member of an HIV-1 circulating BF intersubtype recombinant form family widely spread in South America
inferred← citeshttps://doi.org/10.1038/s42003-025-08687-4openalex-snapshot
Poultry farm density and proximity drive highly pathogenic avian influenza spread
inferred← citeshttps://doi.org/10.1038/s43856-022-00072-0openalex-snapshot
SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal
inferred← citeshttps://doi.org/10.1038/s43856-025-01203-zopenalex-snapshot
First imported cases of MPXV Clade Ib from Goma, Democratic Republic of the Congo
inferred← citeshttps://doi.org/10.1038/srep07630openalex-snapshot
Poultry farms as a source of avian influenza A (H7N9) virus reassortment and human infection
inferred← citeshttps://doi.org/10.1038/srep16897openalex-snapshot
History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region
inferred← citeshttps://doi.org/10.1038/srep44585openalex-snapshot
The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis
inferred← citeshttps://doi.org/10.1038/srep44947openalex-snapshot
The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia
inferred← citeshttps://doi.org/10.1038/srep45505openalex-snapshot
Global evolutionary history and spatio-temporal dynamics of dengue virus type 2
inferred← citeshttps://doi.org/10.1056/nejmoa1804498openalex-snapshot
Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018
inferred← citeshttps://doi.org/10.1071/is14018openalex-snapshot
Discordance between morphological species identification and mtDNA phylogeny in the flesh fly genus Ravinia (Diptera : Sarcophagidae)
inferred← citeshttps://doi.org/10.1071/is15018openalex-snapshot
Evidence from molecules and morphology expands Podonomopsis Brundin (Diptera : Chironomidae : Podonominae) to include ‘genus Chile’
inferred← citeshttps://doi.org/10.1073/pnas.0700741104openalex-snapshot
A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus
inferred← citeshttps://doi.org/10.1073/pnas.0704076104openalex-snapshot
Isolates of Zaire ebolavirus from wild apes reveal genetic lineage and recombinants
inferred← citeshttps://doi.org/10.1073/pnas.0711024105openalex-snapshot
Major evolutionary transitions in ant agriculture
inferred← citeshttps://doi.org/10.1073/pnas.0904991106openalex-snapshot
Dating the emergence of pandemic influenza viruses
inferred← citeshttps://doi.org/10.1073/pnas.1012249108openalex-snapshot
A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries ( Empetrum )
inferred← citeshttps://doi.org/10.1073/pnas.1109314108openalex-snapshot
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans
inferred← citeshttps://doi.org/10.1073/pnas.1202690109openalex-snapshot
Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses
inferred← citeshttps://doi.org/10.1073/pnas.1802028115openalex-snapshot
Phylogenetic approach to recover integration dates of latent HIV sequences within-host
inferred← citeshttps://doi.org/10.1073/pnas.1803990115openalex-snapshot
Structure of the Lassa virus glycan shield provides a model for immunological resistance
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