ArticleGenome biology and evolution2022
A Practical Guide to Design and Assess a Phylogenomic Study.
Article in Genome biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- The Dayhoff Exchange Score: A New Metric to Quantify Entropic Site Saturation in Amino Acid Data Sets Prior to Phylogenetic Analysis.Systematic biology · 2026Article
- Molecular Detection of Filarioid Nematodes in Bats from the Western Brazilian Amazon.Acta parasitologica · 2026Article
- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.Molecular biology and evolution · 2026Article
- Review
- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.bioRxiv : the preprint server for biology · 2026Article
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- OrthoGarden: a pipeline for propagating phylogenetic trees for nonmodel organisms from short reads and de novo genome assemblies.Molecular biology and evolution · 2026Article
- A Practical Guide for Harnessing Phylogenomics in Biocontrol: Accounting for Topological Uncertainty and Phylogenetic Distance in the Centrifugal Phylogenetic Method and Beyond.Evolutionary applications · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- AmpliPhy improves gene trees by adding homologous sequences without affecting alignments.Bioinformatics advances · 2026Article
- Characterization of the complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2026Article
- Phylogenetic Methods Meet Deep Learning.Genome biology and evolution · 2025Article
- Beyond White-Nose Syndrome: Mitochondrial and Functional Genomics ofJournal of fungi (Basel, Switzerland) · 2025Article
- Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics.Genome biology and evolution · 2025Article
- Modeling compositional heterogeneity resolves deep phylogeny of flowering plants.Plant diversity · 2025Article
- Genome Annotation.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida.Proceedings. Biological sciences · 2024Article
- OrthoPhyl-streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales.G3 (Bethesda, Md.) · 2024Article
- Article
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1 author.
Funding
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Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.