Reference health
Nonadaptive Amino Acid Convergence Rates Decrease over Time
38/38 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
7 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 38 checked references that resolve
resolves10.1073/pnas.1314781111
Mutational effects on stability are largely conserved during protein evolution
resolves10.1371/journal.ppat.1000058
Changing Selective Pressure during Antigenic Changes in Human Influenza H3
resolves10.1371/journal.pone.0002201
Adaptive Evolution and Functional Redesign of Core Metabolic Proteins in Snakes
resolves10.1073/pnas.0900233106
Evidence for an ancient adaptive episode of convergent molecular evolution
resolves10.1002/prot.22964
The evolution and evolutionary consequences of marginal thermostability in proteins
resolves10.1093/oxfordjournals.molbev.a025995
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies
resolves10.1007/BF01731581
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
resolves10.1093/molbev/msq047
Statistical Potentials for Improved Structurally Constrained Evolutionary Models
resolves10.1002/(SICI)1097-0134(19980815)32:3<289::AID-PROT4>3.0.CO;2-D
Models of natural mutations including site heterogeneity
resolves10.1089/dna.2004.23.707
Detecting Gradients of Asymmetry in Site-Specific Substitutions in Mitochondrial Genomes
resolves10.1093/molbev/msh112
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
resolves10.1006/jmbi.1999.2962
Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 Å resolution with a μ-(hydr)oxo bridged di-iron center
resolves10.1016/j.cub.2009.11.058
Convergent sequence evolution between echolocating bats and dolphins
resolves10.1073/pnas.0409137102
An algorithm for progressive multiple alignment of sequences with insertions
resolves10.1021/ma00145a039
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
resolves10.1006/jmbi.1998.2601
Coevolving protein residues: maximum likelihood identification and relationship to structure 1 1Edited by G. Von Heijne
resolves10.1093/bioinformatics/btn445
Empirical profile mixture models for phylogenetic reconstruction
resolves10.1093/molbev/msg184
Protein Evolution with Dependence Among Codons Due to Tertiary Structure
resolves10.1371/journal.pgen.1002788
Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales
resolves10.1534/genetics.111.136432
Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models
resolves10.1371/journal.pcbi.1000564
Identifying Changes in Selective Constraints: Host Shifts in Influenza
resolves10.1093/oxfordjournals.molbev.a003851
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
resolves10.1371/journal.pcbi.0020069
Assessing the Accuracy of Ancestral Protein Reconstruction Methods
resolves10.1093/oxfordjournals.molbev.a025888
Models of amino acid substitution and applications to mitochondrial protein evolution
resolves10.1093/gbe/evs085
SP Transcription Factor Paralogs and DNA-Binding Sites Coevolve and Adaptively Converge in Mammals and Birds
The 7 references without a DOI — listed, not checked
no DOI — not checkedSecond international symposium on information theory
no DOI — not checkedInformation measures and model selection
no DOI — not checkedAn introduction to population genetics theory
no DOI — not checkedInferring phylogenies
no DOI — not checkedA codon-based model of nucleotide substitution for protein-coding DNA sequences
no DOI — not checkedAnalyzing site heterogeneity during protein evolution
no DOI — not checkedMrModeltest v2. Program distributed by the author
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