On the public citation graph
Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
0 signed · 59 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.
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known work and none has been retracted — and get a dated CiteStamped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.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/bf01732340openalex-snapshot
Two types of amino acid substitutions in protein evolution
inferredcites →https://doi.org/10.1007/pl00006471openalex-snapshot
Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
inferredcites →https://doi.org/10.1016/j.gene.2005.08.013openalex-snapshot
A close relationship between Cercozoa and Foraminifera supported by phylogenetic analyses based on combined amino acid sequences of three cytoskeletal proteins (actin, α-tubulin, and β-tubulin)
inferredcites →https://doi.org/10.1016/s0959-437x(02)00353-2openalex-snapshot
Evolution of synonymous codon usage in metazoans
inferredcites →https://doi.org/10.1016/s1055-7903(03)00057-5openalex-snapshot
The root of the mammalian tree inferred from whole mitochondrial genomes
inferredcites →https://doi.org/10.1078/1434461042650325openalex-snapshot
Phylogeny of Nuclear-Encoded Plastid-Targeted GAPDH Gene Supports Separate Origins for the Peridinin- and the Fucoxanthin Derivative-Containing Plastids of Dinoflagellates
inferredcites →https://doi.org/10.1080/10635150490468756openalex-snapshot
Phylogenetic Artifacts Can be Caused by Leucine, Serine, and Arginine Codon Usage Heterogeneity: Dinoflagellate Plastid Origins as a Case Study
inferredcites →https://doi.org/10.1080/10635150500354688openalex-snapshot
An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction
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/18.3.502openalex-snapshot
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
inferredcites →https://doi.org/10.1093/bioinformatics/btg180openalex-snapshot
MrBayes 3: Bayesian phylogenetic inference under mixed models
inferredcites →https://doi.org/10.1093/genetics/144.3.1297openalex-snapshot
Molecular Evolution Between Drosophila melanogaster and D. simulans Reduced Codon Bias, Faster Rates of Amino Acid Substitution, and Larger Proteins in D. melanogaster
inferredcites →https://doi.org/10.1093/genetics/148.3.929openalex-snapshot
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene
inferredcites →https://doi.org/10.1093/molbev/msg195openalex-snapshot
Nucleus-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Indicates a Single Origin for Chromalveolate Plastids
inferredcites →https://doi.org/10.1093/molbev/msh065openalex-snapshot
Four New Avian Mitochondrial Genomes Help Get to Basic Evolutionary Questions in the Late Cretaceous
inferredcites →https://doi.org/10.1093/molbev/msh137openalex-snapshot
Genome-Scale Phylogeny and the Detection of Systematic Biases
inferredcites →https://doi.org/10.1093/molbev/msi118openalex-snapshot
Tertiary Endosymbiosis Driven Genome Evolution in Dinoflagellate Algae
inferredcites →https://doi.org/10.1093/molbev/msi172openalex-snapshot
Chlorophyll c–Containing Plastid Relationships Based on Analyses of a Multigene Data Set with All Four Chromalveolate Lineages
inferredcites →https://doi.org/10.1093/molbev/msj021openalex-snapshot
Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences
inferredcites →https://doi.org/10.1093/molbev/msj068openalex-snapshot
Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of “Primitive” Eukaryotes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003818openalex-snapshot
Nuclear-Encoded, Plastid-Targeted Genes Suggest a Single Common Origin for Apicomplexan and Dinoflagellate Plastids
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025991openalex-snapshot
Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040153openalex-snapshot
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040220openalex-snapshot
On the use of nucleic acid sequences to infer early branchings in the tree of life.
inferredcites →https://doi.org/10.1098/rspb.2001.1677openalex-snapshot
Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials
inferredcites →https://doi.org/10.1099/ijs.0.63216-0openalex-snapshot
On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes
inferredcites →https://doi.org/10.1111/j.1550-7408.1999.tb04614.xopenalex-snapshot
Principles of Protein and Lipid Targeting in Secondary Symbiogenesis: Euglenoid, Dinoflagellate, and Sporozoan Plastid Origins and the Eukaryote Family Tree 1 , 2
inferredcites →https://doi.org/10.2216/0031-8884(2005)44[26:potpgc]2.0.co;2openalex-snapshot
Phylogeny of thepsbCgene, coding a photosystem II component CP43, suggests separate origins for the peridinin- and fucoxanthin derivative–containing plastids of dinoflagellates
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.11646/palaeoentomology.3.6.16zenodo-depositor-declared
Fleas are parasitic scorpionflies
inferred← citeshttps://doi.org/10.11646/palaeoentomology.6.1.8zenodo-depositor-declared
Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings
inferred← citeshttps://doi.org/10.1007/978-3-7091-1303-5_13openalex-snapshot
Tertiary Plastid Endosymbioses in Dinoflagellates
inferred← citeshttps://doi.org/10.1007/s00239-009-9225-6openalex-snapshot
What Was the Set of Ubiquitin and Ubiquitin-Like Conjugating Enzymes in the Eukaryote Common Ancestor?
inferred← citeshttps://doi.org/10.1007/s00239-013-9549-0openalex-snapshot
Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary
inferred← citeshttps://doi.org/10.1007/s00239-025-10265-5openalex-snapshot
Gene-Specific Substitution Rates for the Vespertilionidae (Chiroptera: Mammalia) Mitochondrial Genome, with the Description of Three new Mitogenomes
inferred← citeshttps://doi.org/10.1007/s00335-010-9283-5openalex-snapshot
A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals
inferred← citeshttps://doi.org/10.1016/j.bse.2014.07.018openalex-snapshot
The evolution of rbcL: A methodology to follow the evolution patterns of Medicago and Sulla (Fabaceae) genera
inferred← citeshttps://doi.org/10.1016/j.gene.2009.10.001openalex-snapshot
Phylogeny of Asian primate malaria parasites inferred from apicoplast genome-encoded genes with special emphasis on the positions of Plasmodium vivax and P. fragile
inferred← citeshttps://doi.org/10.1016/j.ygeno.2023.110771openalex-snapshot
A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae
inferred← citeshttps://doi.org/10.1016/j.ympev.2007.03.003openalex-snapshot
Sorting wheat from chaff in multi-gene analyses of chlorophyll c-containing plastids
inferred← citeshttps://doi.org/10.1016/j.ympev.2007.05.003openalex-snapshot
Assessing the monophyly of chlorophyll-c containing plastids by multi-gene phylogenies under the unlinked model conditions
inferred← citeshttps://doi.org/10.1016/j.ympev.2020.106782openalex-snapshot
Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)
inferred← citeshttps://doi.org/10.1093/g3journal/jkad299openalex-snapshot
A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH)
inferred← citeshttps://doi.org/10.1093/molbev/mss264openalex-snapshot
A Method of Alignment Masking for Refining the Phylogenetic Signal of Multiple Sequence Alignments
inferred← citeshttps://doi.org/10.1093/molbev/msu105openalex-snapshot
Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins
inferred← citeshttps://doi.org/10.1093/molbev/msx324openalex-snapshot
Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils
inferred← citeshttps://doi.org/10.1093/sysbio/syp006openalex-snapshot
A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion
inferred← citeshttps://doi.org/10.1093/sysbio/sys077openalex-snapshot
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
inferred← citeshttps://doi.org/10.1093/sysbio/syu049openalex-snapshot
Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias
inferred← citeshttps://doi.org/10.1111/j.1529-8817.2008.00559.xopenalex-snapshot
A HYPOTHESIS FOR PLASTID EVOLUTION IN CHROMALVEOLATES1
inferred← citeshttps://doi.org/10.1111/jse.12214openalex-snapshot
Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola
inferred← citeshttps://doi.org/10.1111/jse.12233openalex-snapshot
Relative benefits of amino‐acid, codon, degeneracy, DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons
inferred← citeshttps://doi.org/10.1111/jse.12248openalex-snapshot
Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses
inferred← citeshttps://doi.org/10.1111/nph.15587openalex-snapshot
Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)
inferred← citeshttps://doi.org/10.1111/syen.12569openalex-snapshot
A genome‐wide phylogeny and the diversification of genus Liriomyza (Diptera: Agromyzidae) inferred from anchored phylogenomics
inferred← citeshttps://doi.org/10.1111/syen.12657openalex-snapshot
Lacewing‐specific Universal Single Copy Orthologs designed towards resolution of backbone phylogeny of Neuropterida
inferred← citeshttps://doi.org/10.1186/1471-2148-7-s1-s5openalex-snapshot
Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
inferred← citeshttps://doi.org/10.1371/journal.pone.0023408openalex-snapshot
Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods
inferred← citeshttps://doi.org/10.1534/genetics.107.070466openalex-snapshot
Variable Strength of Translational Selection Among 12 Drosophila Species
inferred← citeshttps://doi.org/10.20944/preprints201910.0086.v1openalex-snapshot
How Codon Usage Bias Affects Our Ability to Recover the Tree of Life
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.