On the public citation graph

Relative model fit does not predict topological accuracy in single-gene protein phylogenetics

https://doi.org/10.1101/698860
0 signed · 89 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/bimj.200810425openalex-snapshot
Simultaneous Inference in General Parametric Models
inferredcites →https://doi.org/10.1007/bf00166252openalex-snapshot
Statistical tests of models of DNA substitution
inferredcites →https://doi.org/10.1007/bf02109483openalex-snapshot
Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
inferredcites →https://doi.org/10.1007/s002399910038openalex-snapshot
Plastid Genome Phylogeny and a Model of Amino Acid Substitution for Proteins Encoded by Chloroplast DNA
inferredcites →https://doi.org/10.1016/0040-5809(84)90027-3openalex-snapshot
Line-of-descent and genealogical processes, and their applications in population genetics models
inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot
Evolution of Protein Molecules
inferredcites →https://doi.org/10.1016/j.cell.2015.07.020openalex-snapshot
Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus
inferredcites →https://doi.org/10.1016/j.cub.2018.11.042openalex-snapshot
A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
inferredcites →https://doi.org/10.1038/nature12130openalex-snapshot
Inferring ancient divergences requires genes with strong phylogenetic signals
inferredcites →https://doi.org/10.1038/nature15697openalex-snapshot
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
inferredcites →https://doi.org/10.1038/nmeth.2109openalex-snapshot
jModelTest 2: more models, new heuristics and parallel computing
inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot
ModelFinder: fast model selection for accurate phylogenetic estimates
inferredcites →https://doi.org/10.1038/nrg.2015.18openalex-snapshot
Causes of evolutionary rate variation among protein sites
inferredcites →https://doi.org/10.1038/s41467-019-08822-wopenalex-snapshot
Model selection may not be a mandatory step for phylogeny reconstruction
inferredcites →https://doi.org/10.1073/pnas.0501865102openalex-snapshot
The application of statistical physics to evolutionary biology
inferredcites →https://doi.org/10.1073/pnas.1518127112openalex-snapshot
Genomic data do not support comb jellies as the sister group to all other animals
inferredcites →https://doi.org/10.1073/pnas.1719358115openalex-snapshot
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
inferredcites →https://doi.org/10.1080/01621459.1987.10478472openalex-snapshot
Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests Under Nonstandard Conditions
inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
An Approximately Unbiased Test of Phylogenetic Tree Selection
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/10.1080/10635150801898920openalex-snapshot
Does Choice in Model Selection Affect Maximum Likelihood Analysis?
inferredcites →https://doi.org/10.1089/10665270050514918openalex-snapshot
Modeling Amino Acid Replacement
inferredcites →https://doi.org/10.1093/acprof:oso/9780199602605.001.0001openalex-snapshot
Molecular Evolution
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/8.3.275openalex-snapshot
The rapid generation of mutation data matrices from protein sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btn445openalex-snapshot
Empirical profile mixture models for phylogenetic reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btr088openalex-snapshot
ProtTest 3: fast selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/gbe/evt151openalex-snapshot
On the Need for Mechanistic Models in Computational Genomics and Metagenomics
inferredcites →https://doi.org/10.1093/gbe/evv261openalex-snapshot
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msi005openalex-snapshot
Different Versions of the Dayhoff Rate Matrix
inferredcites →https://doi.org/10.1093/molbev/msl136openalex-snapshot
MtArt: A New Model of Amino Acid Replacement for Arthropoda
inferredcites →https://doi.org/10.1093/molbev/msn067openalex-snapshot
An Improved General Amino Acid Replacement Matrix
inferredcites →https://doi.org/10.1093/molbev/msq168openalex-snapshot
Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods
inferredcites →https://doi.org/10.1093/molbev/mss112openalex-snapshot
Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates
inferredcites →https://doi.org/10.1093/molbev/mst024openalex-snapshot
Ultrafast Approximation for Phylogenetic Bootstrap
inferredcites →https://doi.org/10.1093/molbev/msu081openalex-snapshot
A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape
inferredcites →https://doi.org/10.1093/molbev/msu173openalex-snapshot
An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
inferredcites →https://doi.org/10.1093/molbev/msu220openalex-snapshot
An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msv003openalex-snapshot
The Relationship between dN/dS and Scaled Selection Coefficients
inferredcites →https://doi.org/10.1093/molbev/msv026openalex-snapshot
The Effects of Partitioning on Phylogenetic Inference
inferredcites →https://doi.org/10.1093/molbev/msv154openalex-snapshot
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations
inferredcites →https://doi.org/10.1093/molbev/msv167openalex-snapshot
Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs
inferredcites →https://doi.org/10.1093/molbev/msv207openalex-snapshot
Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales
inferredcites →https://doi.org/10.1093/molbev/msw171openalex-snapshot
Extensively Parameterized Mutation–Selection Models Reliably Capture Site-Specific Selective Constraint
inferredcites →https://doi.org/10.1093/molbev/msw237openalex-snapshot
Shifting Balance on a Static Mutation–Selection Landscape: A Novel Scenario of Positive Selection
inferredcites →https://doi.org/10.1093/molbev/msw260openalex-snapshot
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
UFBoot2: Improving the Ultrafast Bootstrap Approximation
inferredcites →https://doi.org/10.1093/molbev/msx286openalex-snapshot
P3: Phylogenetic Posterior Prediction in RevBayes
inferredcites →https://doi.org/10.1093/molbev/msy049openalex-snapshot
Phenomenological Load on Model Parameters Can Lead to False Biological Conclusions
inferredcites →https://doi.org/10.1093/molbev/msy127openalex-snapshot
Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model
inferredcites →https://doi.org/10.1093/molbev/msz189openalex-snapshot
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
inferredcites →https://doi.org/10.1093/nar/gkj087openalex-snapshot
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004175openalex-snapshot
Bayesian Model Adequacy and Choice in Phylogenetics
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025888openalex-snapshot
Models of amino acid substitution and applications to mitochondrial protein evolution
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025995openalex-snapshot
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies
inferredcites →https://doi.org/10.1093/sysbio/syu009openalex-snapshot
Predictive Approaches to Assessing the Fit of Evolutionary Models
inferredcites →https://doi.org/10.1093/sysbio/syu062openalex-snapshot
ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1098/rstb.2008.0162openalex-snapshot
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
inferredcites →https://doi.org/10.1098/rstb.2008.0175openalex-snapshot
Bayesian analysis of amino acid substitution models
inferredcites →https://doi.org/10.1098/rstb.2008.0180openalex-snapshot
Phylogenetic mixture models for proteins
inferredcites →https://doi.org/10.1126/science.1242592openalex-snapshot
The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110617-062249openalex-snapshot
Evaluating Model Performance in Evolutionary Biology
inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152633openalex-snapshot
Model Selection in Phylogenetics
inferredcites →https://doi.org/10.1186/1471-2148-10-242openalex-snapshot
Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets
inferredcites →https://doi.org/10.1186/1471-2148-10-99openalex-snapshot
FLU, an amino acid substitution model for influenza proteins
inferredcites →https://doi.org/10.1186/1471-2148-14-23openalex-snapshot
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
inferredcites →https://doi.org/10.1186/1471-2148-6-29openalex-snapshot
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
inferredcites →https://doi.org/10.1186/s12862-017-0987-yopenalex-snapshot
Improved mitochondrial amino acid substitution models for metazoan evolutionary studies
inferredcites →https://doi.org/10.1201/9780429258411openalex-snapshot
Bayesian Data Analysis
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pone.0000503openalex-snapshot
HIV-Specific Probabilistic Models of Protein Evolution
inferredcites →https://doi.org/10.1371/journal.pone.0139047openalex-snapshot
Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies
inferredcites →https://doi.org/10.1371/journal.ppat.1006114openalex-snapshot
Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture
inferredcites →https://doi.org/10.1534/genetics.111.128025openalex-snapshot
The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution
inferredcites →https://doi.org/10.1534/genetics.111.136432openalex-snapshot
Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models
inferredcites →https://doi.org/10.1534/genetics.115.185264openalex-snapshot
A Comparison of One-Rate and Two-Rate Inference Frameworks for Site-Specific dN/ dS Estimation
inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot
Fitting Linear Mixed-Effects Models Using lme4
inferredcites →https://doi.org/10.21105/joss.01686openalex-snapshot
Welcome to the Tidyverse
inferredcites →https://doi.org/10.3389/fgene.2015.00319openalex-snapshot
Trends in substitution models of molecular evolution
inferredcites →https://doi.org/10.3390/computation3020177openalex-snapshot
A Guide to Phylogenetic Reconstruction Using Heterogeneous Models—A Case Study from the Root of the Placental Mammal Tree
inferredcites →https://doi.org/10.7554/elife.03300openalex-snapshot
The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin
inferredcites →https://doi.org/10.7554/elife.34420openalex-snapshot
Mapping mutational effects along the evolutionary landscape of HIV envelope

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/2020.01.09.899906openalex-snapshot
ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning
inferred← citeshttps://doi.org/10.1101/2020.02.14.949339openalex-snapshot
Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.