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An experimental phylogeny to benchmark ancestral sequence reconstruction

35/35 checkable references clean · checked 2026-08-30

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.

The 35 checked references that resolve

resolves10.1038/nrg1324

Resurrecting ancient genes: experimental analysis of extinct molecules

resolves10.7554/eLife.10147

Evolution of an ancient protein function involved in organized multicellularity in animals

resolves10.1111/evo.12794

The molecular origin and evolution of dim-light vision in mammals

resolves10.1007/s00239-015-9697-5

Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties

resolves10.1073/pnas.1320393111

Evolutionary history and metabolic insights of ancient mammalian uricases

resolves10.1126/science.aaa1823

Using ancient protein kinases to unravel a modern cancer drug’s mechanism

resolves10.1038/nrg2160

Mechanistic approaches to the study of evolution: the functional synthesis

resolves10.1126/science.1736360

Experimental Phylogenetics: Generation of a Known Phylogeny

resolves10.1073/pnas.96.20.11241

Circular permutation and receptor insertion within green fluorescent proteins

resolves10.1073/pnas.082243699

A monomeric red fluorescent protein

resolves10.1093/molbev/msq081

Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty

resolves10.1534/genetics.115.177386

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution

resolves10.1371/journal.pcbi.0020069

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

resolves10.1016/0169-5347(96)10041-0

Among-site rate variation and its impact on phylogenetic analyses

resolves10.1093/bioinformatics/btp368

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

resolves10.1093/molbev/msu305

Toward More Accurate Ancestral Protein Genotype–Phenotype Reconstructions with the Use of Species Tree-Aware Gene Trees

resolves10.1371/journal.pone.0002680

Diversity and Evolution of Coral Fluorescent Proteins

resolves10.1093/nar/gks498

FastML: a web server for probabilistic reconstruction of ancestral sequences

resolves10.1093/genetics/141.4.1641

A new method of inference of ancestral nucleotide and amino acid sequences.

resolves10.1080/10635150290102357

Increased Taxon Sampling Is Advantageous for Phylogenetic Inference

resolves10.1080/106351598260987

Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias

resolves10.1080/106351598261021

Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators

resolves10.1073/pnas.191248498

Incomplete taxon sampling is not a problem for phylogenetic inference

resolves10.1186/1471-2164-16-S10-S9

Reconstruction of an ancestral Yersinia pestisgenome and comparison with an ancient sequence

resolves10.3390/genes3030423

REGEN: Ancestral Genome Reconstruction for Bacteria

resolves10.1371/journal.pone.0108796

Reconstruction of Ancestral Gene Orders Using Probabilistic and Gene Encoding Approaches

resolves10.1002/pro.2886

Selection on protein structure, interaction, and sequence

resolves10.1073/pnas.1120084109

Amino acid coevolution induces an evolutionary Stokes shift

resolves10.1093/protein/gzv038

Assessing the prediction fidelity of ancestral reconstruction by a library approach

resolves10.1016/j.cbpa.2011.03.005

Utilizing natural diversity to evolve protein function: applications towards thermostability

resolves10.1007/s00239-010-9415-2

Exploiting Models of Molecular Evolution to Efficiently Direct Protein Engineering

resolves10.1038/nbt1037

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein

resolves10.1093/bioinformatics/btr088

ProtTest 3: fast selection of best-fit models of protein evolution

resolves10.1038/nprot.2014.054

Engineering and characterizing monomeric fluorescent proteins for live-cell imaging applications

resolves10.1038/nprot.2013.087

Relative and absolute determination of fluorescence quantum yields of transparent samples

What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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