Reference health
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
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Every reference with a DOI or an arXiv id 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.
2 with no DOI or arXiv id: not checked. A reference deposited without a DOI is checked only when it names an arXiv id, under that id’s DataCite DOI. The rest are never matched by title or guessed at; they stay outside the checked set, and this line says so.
The 49 checked references that resolve
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Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
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MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda
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Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic
resolves10.1093/sysbio/syr064
A Method for Inferring the Rate of Evolution of Homologous Characters that Can Potentially Improve Phylogenetic Inference, Resolve Deep Divergence and Correct Systematic Biases
resolves10.1016/S0723-2020(11)80247-X
Reduced Thermophilic Bias in the 16S rDNA Sequence from Thermus ruber Provides Further Support for a Relationship Between Thermus and Deinococcus
resolves10.1073/pnas.0306212101
The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships
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The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods
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Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
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Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria
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Inferring phylogenies from DNA sequences of unequal base compositions.
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A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods
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Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I
resolves10.1016/j.ympev.2006.03.020
Phylogenetic estimation under codon models can be biased by codon usage heterogeneity
resolves10.1080/10635150490468756
Phylogenetic Artifacts Can be Caused by Leucine, Serine, and Arginine Codon Usage Heterogeneity: Dinoflagellate Plastid Origins as a Case Study
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The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated
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PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
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A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
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Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
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Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence
resolves10.1098/rspb.2004.2917
Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic
resolves10.1038/nature08742
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resolves10.1093/sysbio/syp015
Statistical Comparison of Nucleotide, Amino Acid, and Codon Substitution Models for Evolutionary Analysis of Protein-Coding Sequences
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Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships
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Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda
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Archaeal Phylogeny: Reexamination of the Phylogenetic Position of Archaeoglohus fulgidus in Light of Certain Composition-induced Artifacts
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Models of amino acid substitution and applications to mitochondrial protein evolution
The 2 references with no DOI or arXiv id, listed, not checked
no DOI — not checkedThe rapid generation of mutation data matrices from protein sequences
no DOI — not checkedOn the use of nucleic acid sequences to infer early branches in the tree of life
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