Reference health
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
68/68 checkable references clean · checked 2026-08-23
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.
8 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 68 checked references that resolve
resolves10.1038/nature06614
Broad phylogenomic sampling improves resolution of the animal tree of life
resolves10.1016/j.cub.2009.02.052
Phylogenomics Revives Traditional Views on Deep Animal Relationships
resolves10.1371/journal.pbio.1000020
Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis
resolves10.1242/dev.1994.Supplement.15
Can the Cambrian explosion be inferred through molecular phylogeny?
resolves10.1007/BF02099966
The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence
resolves10.2307/2412923
Cases in which Parsimony or Compatibility Methods Will be Positively Misleading
resolves10.1016/j.tree.2009.01.009
Gene tree discordance, phylogenetic inference and the multispecies coalescent
resolves10.1111/j.1558-5646.2008.00414.x
ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA
resolves10.1016/j.tig.2008.08.009
The quest for orthologs: finding the corresponding gene across genomes
resolves10.1093/nar/29.1.22
The COG database: new developments in phylogenetic classification of proteins from complete genomes
resolves10.1186/1471-2105-10-219
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics
resolves10.1093/molbev/msm070
Glass Sponges and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution?
resolves10.1006/mpev.1996.0036
Early Evolution of the Metazoa and Phylogenetic Status of Diploblasts as Inferred from Amino Acid Sequence of Elongation Factor-1α
resolves10.1073/pnas.171316998
Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA
resolves10.1046/j.1525-142X.2003.03042.x
Conflicting phylogenetic signals at the base of the metazoan tree
resolves10.1093/molbev/msp148
Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa
resolves10.1080/10635150701546231
A Model of Horizontal Gene Transfer and the Bacterial Phylogeny Problem
resolves10.1016/S0168-9525(01)02522-7
Eubacterial phylogeny based on translational apparatus proteins
resolves10.1073/pnas.0602076103
Mitochondrial genome of
<i>Trichoplax adhaerens</i>
supports Placozoa as the basal lower metazoan phylum
resolves10.1093/molbev/msq089
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
resolves10.1093/molbev/msl137
Lack of Resolution in the Animal Phylogeny: Closely Spaced Cladogeneses or Undetected Systematic Errors?
resolves10.1080/10635150500234583
Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?
resolves10.1093/sysbio/syp017
The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
resolves10.1186/1471-2148-8-95
Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
resolves10.1093/molbev/msh182
Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments
resolves10.1093/oxfordjournals.molbev.a003851
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
resolves10.1093/molbev/msh112
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
resolves10.1098/rspb.2009.0896
Assessing the root of bilaterian animals with scalable phylogenomic methods
resolves10.1046/j.1420-9101.1994.7020247.x
Comparison of molecular and paleontological data in diatoms suggests a major gap in the fossil record
resolves10.1186/1748-7188-5-37
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
resolves10.1093/oxfordjournals.molbev.a026334
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
resolves10.1186/1471-2148-7-S1-S2
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
resolves10.1073/pnas.032662799
The analysis of 100 genes supports the grouping of three highly divergent amoebae:
<i>Dictyostelium</i>
,
<i>Entamoeba</i>
, and
<i>Mastigamoeba</i>
resolves10.1093/molbev/msg184
Protein Evolution with Dependence Among Codons Due to Tertiary Structure
resolves10.1093/molbev/msl041
Assessing Site-Interdependent Phylogenetic Models of Sequence Evolution
resolves10.1098/rstb.2008.0163
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures
resolves10.1093/molbev/msp228
Rapid Likelihood Analysis on Large Phylogenies Using Partial Sampling of Substitution Histories
resolves10.1073/pnas.92.24.11317
Inferring phylogenies from DNA sequences of unequal base compositions.
resolves10.1016/0169-5347(96)10041-0
Among-site rate variation and its impact on phylogenetic analyses
resolves10.1093/molbev/msn042
A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy
resolves10.1080/10635150701397643
Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
resolves10.1093/bioinformatics/bti191
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
resolves10.1093/bioinformatics/btp368
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
The 8 references without a DOI — listed, not checked
no DOI — not checkedHow much can evolved characters tell us about the tree that generated them?
no DOI — not checkedCurrent approaches to phylogenomic reconstruction.
no DOI — not checkedInferring phylogenies
no DOI — not checkedGraph clustering by flow simulation [PhD dissertation]
no DOI — not checkedMissing data and the accuracy of Bayesian phylogenetics.
no DOI — not checkedEvolution of protein molecules.
no DOI — not checkedA model of evolutionary change in proteins.
no DOI — not checkedOn the use of nucleic acid sequences to infer early branchings in the tree of life.
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