{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T03:04:08Z","timestamp":1792292648535,"version":"4.4.0"},"reference-count":235,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T00:00:00Z","timestamp":1660089600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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 \u201cbig data\u201d 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 \u201cmore genes, more robustness\u201d 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.<\/jats:p>","DOI":"10.1093\/gbe\/evac129","type":"journal-article","created":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T07:28:48Z","timestamp":1660116528000},"source":"Crossref","is-referenced-by-count":78,"title":["A Practical Guide to Design and Assess a Phylogenomic Study"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3597-1221","authenticated-orcid":false,"given":"Jesus","family":"Lozano-Fernandez","sequence":"first","affiliation":[{"name":"Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona , Avd. Diagonal 643, 08028 Barcelona , Spain"},{"name":"Institute of Evolutionary Biology (CSIC \u2013 Universitat Pompeu Fabra) , Passeig mar\u00edtim de la Barcelona 37-49, 08003 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,8,10]]},"reference":[{"issue":"6632","key":"2022090805181075700_evac129-B1","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1038\/387489a0","article-title":"Evidence for a clade of nematodes, arthropods and other moulting animals","volume":"387","author":"Aguinaldo","year":"1997","journal-title":"Nature."},{"key":"2022090805181075700_evac129-B2","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1007\/s00239-020-09969-7","article-title":"A phylogenetic rate parameter indicates different sequence divergence patterns in orthologs and paralogs","volume":"88","author":"Ahrens","year":"2020","journal-title":"J Mol Evol."},{"key":"2022090805181075700_evac129-B3","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nmeth.3830","article-title":"Standardized benchmarking in the quest for orthologs","volume":"13","author":"Altenhoff","year":"2016","journal-title":"Nat Methods."},{"issue":"2","key":"2022090805181075700_evac129-B4","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1093\/molbev\/msl170","article-title":"Bayesian estimation of concordance among gene trees","volume":"24","author":"An\u00e9","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2022090805181075700_evac129-B5","doi-asserted-by":"crossref","DOI":"10.1038\/s41559-016-0020","article-title":"Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life","volume":"1","author":"Arcila","year":"2017","journal-title":"Nat Ecol Evol"},{"issue":"5","key":"2022090805181075700_evac129-B6","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"issue":"1","key":"2022090805181075700_evac129-B7","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1093\/molbev\/msl137","article-title":"Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?","volume":"24","author":"Baurain","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2022090805181075700_evac129-B8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-57249-2","article-title":"Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae","volume":"10","author":"Bellot","year":"2020","journal-title":"Sci Rep"},{"issue":"2","key":"2022090805181075700_evac129-B9","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1096-0031.2005.00059.x","article-title":"A review of long-branch attraction","volume":"21","author":"Bergsten","year":"2005","journal-title":"Cladistics."},{"issue":"2","key":"2022090805181075700_evac129-B10","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1093\/sysbio\/syt073","article-title":"Conserved genes, sampling error, and phylogenomic inference","volume":"63","author":"Betancur-R","year":"2014","journal-title":"Syst Biol"},{"key":"2022090805181075700_evac129-B11","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1093\/oxfordjournals.molbev.a004175","article-title":"Bayesian model adequacy and choice in phylogenetics","volume":"19","author":"Bollback","year":"2002","journal-title":"Mol Biol Evol"},{"key":"2022090805181075700_evac129-B12","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.ympev.2017.03.022","article-title":"The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data","volume":"111","author":"Bossert","year":"2017","journal-title":"Mol Phylogenet Evol"},{"issue":"2","key":"2022090805181075700_evac129-B13","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1101\/gr.141978.112","article-title":"Genome-scale coestimation of species and gene trees","volume":"23","author":"Boussau","year":"2013","journal-title":"Genome Res"},{"issue":"7","key":"2022090805181075700_evac129-B14","doi-asserted-by":"crossref","first-page":"e6399","DOI":"10.7717\/peerj.6399","article-title":"Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics","volume":"14","author":"Bravo","year":"2019","journal-title":"PeerJ."},{"issue":"6","key":"2022090805181075700_evac129-B15","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1093\/oxfordjournals.molbev.a026166","article-title":"Archaea sister group of Bacteria? 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