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Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Identification of common molecular subsequences
inferredcites →https://doi.org/10.1016/j.tig.2007.08.014openalex-snapshot
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nature08182openalex-snapshot
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
inferredcites →https://doi.org/10.1038/nature09014openalex-snapshot
A formal test of the theory of universal common ancestry
inferredcites →https://doi.org/10.1073/pnas.1323926111openalex-snapshot
Phylotranscriptomic analysis of the origin and early diversification of land plants
inferredcites →https://doi.org/10.1080/10635150490445779openalex-snapshot
Modeling Compositional Heterogeneity
inferredcites →https://doi.org/10.1093/bioinformatics/btg213openalex-snapshot
Detecting putative orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btm585openalex-snapshot
Choosing BLAST options for better detection of orthologs as reciprocal best hits
inferredcites →https://doi.org/10.1093/bioinformatics/btu492openalex-snapshot
Big data and other challenges in the quest for orthologs
inferredcites →https://doi.org/10.1093/molbev/msn214openalex-snapshot
An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases
inferredcites →https://doi.org/10.1093/molbev/mst117openalex-snapshot
Heterogeneous Models Place the Root of the Placental Mammal Phylogeny
inferredcites →https://doi.org/10.1093/molbev/msu245openalex-snapshot
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
inferredcites →https://doi.org/10.1093/molbev/msu286openalex-snapshot
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
inferredcites →https://doi.org/10.1093/molbev/msv081openalex-snapshot
Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing
inferredcites →https://doi.org/10.1093/nar/gkj123openalex-snapshot
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
inferredcites →https://doi.org/10.1093/nar/gkq1238openalex-snapshot
OMA 2011: orthology inference among 1000 complete genomes
inferredcites →https://doi.org/10.1093/nar/gkt1253openalex-snapshot
eggNOG v4.0: nested orthology inference across 3686 organisms
inferredcites →https://doi.org/10.1093/nar/gku1203openalex-snapshot
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
inferredcites →https://doi.org/10.1093/nar/gku1220openalex-snapshot
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003974openalex-snapshot
Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026389openalex-snapshot
Estimation of Primate Speciation Dates Using Local Molecular Clocks
inferredcites →https://doi.org/10.1093/sysbio/syq037openalex-snapshot
Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life
inferredcites →https://doi.org/10.1093/sysbio/syu126openalex-snapshot
Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites
inferredcites →https://doi.org/10.1098/rstb.2008.0162openalex-snapshot
Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.8.3.163openalex-snapshot
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
inferredcites →https://doi.org/10.1126/science.1163197openalex-snapshot
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1146/annurev.genom.1.1.41openalex-snapshot
Gene Family Evolution and Homology: Genomics Meets Phylogenetics
inferredcites →https://doi.org/10.1186/1471-2105-12-221openalex-snapshot
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
inferredcites →https://doi.org/10.1186/1471-2105-14-330openalex-snapshot
Agalma: an automated phylogenomics workflow
inferredcites →https://doi.org/10.1186/1471-2105-8-83openalex-snapshot
Orthology prediction at scalable resolution by phylogenetic tree analysis
inferredcites →https://doi.org/10.1186/1471-2148-9-157openalex-snapshot
HaMStR: Profile hidden markov model based search for orthologs in ESTs
inferredcites →https://doi.org/10.1186/1741-7007-8-114openalex-snapshot
Bayesian random local clocks, or one rate to rule them all
inferredcites →https://doi.org/10.1186/1741-7007-8-66openalex-snapshot
Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa
inferredcites →https://doi.org/10.1186/1742-9994-10-1openalex-snapshot
Dispersal and gene flow in free-living marine nematodes
inferredcites →https://doi.org/10.1186/1742-9994-10-18openalex-snapshot
Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems
inferredcites →https://doi.org/10.1186/1745-6150-6-60openalex-snapshot
On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
inferredcites →https://doi.org/10.1186/s13059-014-0572-2openalex-snapshot
De novo assembly of bacterial transcriptomes from RNA-seq data
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1371/journal.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pbio.1000602openalex-snapshot
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
inferredcites →https://doi.org/10.1371/journal.pgen.1002411openalex-snapshot
A Functional Phylogenomic View of the Seed Plants
inferredcites →https://doi.org/10.1371/journal.pone.0054583openalex-snapshot
Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results
inferredcites →https://doi.org/10.1371/journal.pone.0056925openalex-snapshot
The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: A Simulation Study
inferredcites →https://doi.org/10.2307/2412448openalex-snapshot
Distinguishing Homologous from Analogous Proteins
inferredcites →https://doi.org/10.3724/sp.j.1002.2008.08016openalex-snapshot
Taxon sampling and the accuracy of phylogenetic analyses
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1186/s12862-022-02004-xzenodo-depositor-declared
Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.1002/ajb2.1069openalex-snapshot
From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales
inferred← citeshttps://doi.org/10.1002/bies.202400146openalex-snapshot
Orphan genes are not a distinct biological entity
inferred← citeshttps://doi.org/10.1002/wdev.359openalex-snapshot
The significance of sponges for comparative studies of developmental evolution
inferred← citeshttps://doi.org/10.1007/s00239-025-10254-8openalex-snapshot
Refined Phylogenetic Ortholog Inference Reveals Coevolutionary Expansion of the MAPK Signaling Network Through Finetuning of Pathway Specificity
inferred← citeshttps://doi.org/10.1016/j.cell.2017.09.030openalex-snapshot
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
inferred← citeshttps://doi.org/10.1038/s41598-017-13236-zopenalex-snapshot
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty704openalex-snapshot
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz171openalex-snapshot
phylostratr : a framework for phylostratigraphy
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz799openalex-snapshot
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
inferred← citeshttps://doi.org/10.1093/gbe/evy231openalex-snapshot
From de novo to ‘de nono’: The majority of novel protein coding genes identified with phylostratigraphy are old genes or recent duplicates
inferred← citeshttps://doi.org/10.1093/molbev/msad175openalex-snapshot
Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling
inferred← citeshttps://doi.org/10.1093/molbev/msae111openalex-snapshot
phyloBARCODER: A Web Tool for Phylogenetic Classification of Eukaryote Metabarcodes Using Custom Reference Databases
inferred← citeshttps://doi.org/10.1093/sysbio/syac043openalex-snapshot
Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)
inferred← citeshttps://doi.org/10.1093/sysbio/syy022openalex-snapshot
Phylogenomic Analysis of the Explosive Adaptive Radiation of the Espeletia Complex (Asteraceae) in the Tropical Andes
inferred← citeshttps://doi.org/10.1101/2020.04.20.049999openalex-snapshot
Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices
inferred← citeshttps://doi.org/10.1101/2025.08.19.670927openalex-snapshot
CSI-SSU: Phylogenetic contamination screening of genomic datasets, demonstrated on the Protist 10,000 Genomes (P10K) database
inferred← citeshttps://doi.org/10.1111/1755-0998.13180openalex-snapshot
Hemiptera phylogenomic resources: Tree‐based orthology prediction and conserved exon identification
inferred← citeshttps://doi.org/10.1111/zsc.12211openalex-snapshot
Comparative genomics and the diversity of life
inferred← citeshttps://doi.org/10.1128/spectrum.00866-25openalex-snapshot
Discovery of diverse anellovirus sequences in Thai human sequencing data
inferred← citeshttps://doi.org/10.1186/s12859-017-1726-5openalex-snapshot
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001922openalex-snapshot
Four principles to establish a universal virus taxonomy
inferred← citeshttps://doi.org/10.32469/10355/64234openalex-snapshot
C4 photosynthetic evolution : sub-types, diversity, and function within the grass tribe Paniceae
inferred← citeshttps://doi.org/10.3389/fbinf.2022.871393openalex-snapshot
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
inferred← citeshttps://doi.org/10.3390/genes10040294openalex-snapshot
ORTHOSCOPE Analysis Reveals the Presence of the Cellulose Synthase Gene in All Tunicate Genomes but Not in Other Animal Genomes
inferred← citeshttps://doi.org/10.3390/ijms222111640openalex-snapshot
Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661574openalex-snapshot
Additional file 10 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661577openalex-snapshot
Additional file 11 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661580openalex-snapshot
Additional file 12 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661583openalex-snapshot
Additional file 13 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661586openalex-snapshot
Additional file 14 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661589openalex-snapshot
Additional file 1 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661592openalex-snapshot
Additional file 2 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661595openalex-snapshot
Additional file 3 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661598openalex-snapshot
Additional file 4 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661601openalex-snapshot
Additional file 5 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661604openalex-snapshot
Additional file 6 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661607openalex-snapshot
Additional file 7 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661610openalex-snapshot
Additional file 8 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
inferred← citeshttps://doi.org/10.6084/m9.figshare.19661613openalex-snapshot
Additional file 9 of Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra
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