ArticleNature communications2020
An investigation of irreproducibility in maximum likelihood phylogenetic inference.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.Molecular biology and evolution · 2026Article
- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.bioRxiv : the preprint server for biology · 2026Article
- Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria.Molecular ecology resources · 2026Article
- phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison.Current issues in molecular biology · 2026Article
- Bit-reproducible parallel phylogenetic tree inference.Bioinformatics (Oxford, England) · 2026Article
- A universal polyphosphate kinase powers in vitro transcription.Nature communications · 2026Article
- Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina).Biochemical genetics · 2025Article
- Genetic Evidence ofGenes · 2025Article
- Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae).BMC plant biology · 2025Article
- Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.Proteins · 2025Article
- FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis.Journal of microbiology (Seoul, Korea) · 2025Article
- A vector representation for phylogenetic trees.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics.Systematic biology · 2024Article
- Genome-Wide Analysis of Aquaporins Gene Family inInternational journal of molecular sciences · 2024Article
- The Mitochondrial Genome ofInternational journal of molecular sciences · 2024Article
- Common Methods for Phylogenetic Tree Construction and Their Implementation in R.Bioengineering (Basel, Switzerland) · 2024Review
- Identification of miRNA858 long-loop precursors in seed plants.The Plant cell · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Fusang: a framework for phylogenetic tree inference via deep learning.Nucleic acids research · 2023Article
- Computational Reproducibility of Molecular Phylogenies.Molecular biology and evolution · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates (Run1 and Run2) for each of 19,414 gene alignments in 15 animal, plant, and fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and Run2 sets of individual gene trees are topologically irreproducible for 9/15 phylogenomic datasets, whereas concatenation-based phylogenies inferred twice from the same supermatrix are reproducible. Our simulations further show that irreproducible phylogenies are more likely to be incorrect than reproducible phylogenies. These results suggest that a considerable fraction of single-gene ML trees may be irreproducible. Increasing reproducibility in ML inference will benefit from providing analyses' log files, which contain typically reported parameters (e.g., program, substitution model, number of tree searches) but also typically unreported ones (e.g., random starting seed number, number of threads, processor type).
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