{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T03:07:01Z","timestamp":1767236821010,"version":"3.48.0"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01AI105185"],"award-info":[{"award-number":["R01AI105185"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Evol"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s00239-025-10281-5","type":"journal-article","created":{"date-parts":[[2025,12,27]],"date-time":"2025-12-27T01:11:02Z","timestamp":1766797862000},"page":"830-842","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Quantifying Hierarchical Conflicts in Homology Statements"],"prefix":"10.1007","volume":"93","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8690-1261","authenticated-orcid":false,"given":"Krister M.","family":"Swenson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Afif","family":"Elghraoui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faramarz","family":"Valafar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siavash","family":"Mirarab","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathias","family":"Weller","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,12,27]]},"reference":[{"issue":"5","key":"10281_CR1","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/nmeth.3830","volume":"13","author":"AM Altenhoff","year":"2016","unstructured":"Altenhoff AM, Boeckmann B, Capella-Gutierrez S et al (2016) Standardized benchmarking in the quest for orthologs. Nat Methods 13(5):425\u2013430. https:\/\/doi.org\/10.1038\/nmeth.3830","journal-title":"Nat Methods"},{"issue":"3","key":"10281_CR2","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1093\/bioinformatics\/btq665","volume":"27","author":"SV Angiuoli","year":"2011","unstructured":"Angiuoli SV, Salzberg SL (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27(3):334\u2013342. https:\/\/doi.org\/10.1093\/bioinformatics\/btq665","journal-title":"Bioinformatics"},{"issue":"7833","key":"10281_CR3","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/s41586-020-2871-y","volume":"587","author":"J Armstrong","year":"2020","unstructured":"Armstrong J, Hickey G, Diekhans M et al (2020) Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587(7833):246\u2013251. https:\/\/doi.org\/10.1038\/s41586-020-2871-y. (number: 7833 Publisher: Nature Publishing Group)","journal-title":"Nature"},{"key":"10281_CR4","doi-asserted-by":"publisher","unstructured":"Babenko M, Gusakov A (2011) New exact and approximation algorithms for the star packing problem in undirected graphs. In: Symposium on theoretical aspects of computer science (STACS2011), pp 519\u2013530, https:\/\/doi.org\/10.4230\/LIPIcs.STACS.2011.519","DOI":"10.4230\/LIPIcs.STACS.2011.519"},{"issue":"32","key":"10281_CR5","doi-asserted-by":"publisher","first-page":"10008","DOI":"10.1073\/pnas.1513033112","volume":"112","author":"M Berney","year":"2015","unstructured":"Berney M, Berney-Meyer L, Wong KW et al (2015) Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis. Proc Natl Acad Sci USA 112(32):10008\u201310013. https:\/\/doi.org\/10.1073\/pnas.1513033112. (publisher: National Academy of Sciences Section: Biological Sciences)","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"10281_CR6","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Kent WJ, Riemer C et al (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14(4):708\u2013715. https:\/\/doi.org\/10.1101\/gr.1933104","journal-title":"Genome Res"},{"issue":"6","key":"10281_CR7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147","volume":"5","author":"AE Darling","year":"2010","unstructured":"Darling AE, Mau B, Perna NT (2010) progressivemauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5(6):e11147. https:\/\/doi.org\/10.1371\/journal.pone.0011147","journal-title":"PLoS ONE"},{"key":"10281_CR8","doi-asserted-by":"publisher","unstructured":"Drange PG, Reidl F, S\u00e1nchez Villaamil F, et al (2015) Fast Biclustering by dual parameterization. In: 10th International symposium on parameterized and exact computation (IPEC 2015), Leibniz international proceedings in informatics (LIPIcs), vol\u00a043. Schloss Dagstuhl \u2013 Leibniz-Zentrum f\u00fcr Informatik, Dagstuhl, Germany, pp 402\u2013413, https:\/\/doi.org\/10.4230\/LIPIcs.IPEC.2015.402","DOI":"10.4230\/LIPIcs.IPEC.2015.402"},{"issue":"4","key":"10281_CR9","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1101\/gr.081778.108","volume":"19","author":"I Dubchak","year":"2009","unstructured":"Dubchak I, Poliakov A, Kislyuk A et al (2009) Multiple whole-genome alignments without a reference organism. Genome Res 19(4):682\u2013689. https:\/\/doi.org\/10.1101\/gr.081778.108","journal-title":"Genome Res"},{"issue":"12","key":"10281_CR10","doi-asserted-by":"publisher","first-page":"2077","DOI":"10.1101\/gr.174920.114","volume":"24","author":"D Earl","year":"2014","unstructured":"Earl D, Nguyen N, Hickey G et al (2014) Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res 24(12):2077\u20132089. https:\/\/doi.org\/10.1101\/gr.174920.114","journal-title":"Genome Res"},{"key":"10281_CR11","doi-asserted-by":"publisher","unstructured":"Elghraoui A, Mirarab S, Swenson KM, et al (2022) Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. bioRxiv https:\/\/doi.org\/10.1101\/2022.02.18.481113","DOI":"10.1101\/2022.02.18.481113"},{"issue":"12","key":"10281_CR12","doi-asserted-by":"publisher","first-page":"i9","DOI":"10.1093\/bioinformatics\/btu259","volume":"30","author":"CG Ghiurcuta","year":"2014","unstructured":"Ghiurcuta CG, Moret BM (2014) Evaluating synteny for improved comparative studies. Bioinformatics 30(12):i9\u2013i18. https:\/\/doi.org\/10.1093\/bioinformatics\/btu259","journal-title":"Bioinformatics"},{"issue":"10","key":"10281_CR13","doi-asserted-by":"publisher","first-page":"2157","DOI":"10.1093\/molbev\/msz150","volume":"36","author":"N Glover","year":"2019","unstructured":"Glover N, Dessimoz C, Ebersberger I et al (2019) Advances and applications in the quest for orthologs. Mol Biol Evol 36(10):2157\u20132164. https:\/\/doi.org\/10.1093\/molbev\/msz150","journal-title":"Mol Biol Evol"},{"issue":"1","key":"10281_CR14","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1186\/s12859-014-0354-6","volume":"15","author":"F Hu","year":"2014","unstructured":"Hu F, Lin Y, Tang J (2014) MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinform 15(1):354. https:\/\/doi.org\/10.1186\/s12859-014-0354-6","journal-title":"BMC Bioinform"},{"issue":"15","key":"10281_CR15","doi-asserted-by":"publisher","first-page":"6359","DOI":"10.1093\/nar\/gkr334","volume":"39","author":"J Kim","year":"2011","unstructured":"Kim J, Ma J (2011) PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Res 39(15):6359\u20136368. https:\/\/doi.org\/10.1093\/nar\/gkr334","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"10281_CR16","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1137\/0212040","volume":"12","author":"DG Kirkpatrick","year":"1983","unstructured":"Kirkpatrick DG, Hell P (1983) On the complexity of general graph factor problems. SIAM J Comput 12(3):601\u2013609","journal-title":"SIAM J Comput"},{"key":"10281_CR17","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.dam.2024.01.028","volume":"348","author":"I Koch","year":"2024","unstructured":"Koch I, Pardal N, dos Santos VF (2024) Edge deletion to tree-like graph classes. Discret Appl Math 348:122\u2013131. https:\/\/doi.org\/10.1016\/j.dam.2024.01.028","journal-title":"Discret Appl Math"},{"issue":"11","key":"10281_CR18","doi-asserted-by":"publisher","first-page":"1720","DOI":"10.1101\/gr.236273.118","volume":"28","author":"M Kolmogorov","year":"2018","unstructured":"Kolmogorov M, Armstrong J, Raney BJ et al (2018) Chromosome assembly of large and complex genomes using multiple references. Genome Res 28(11):1720\u20131732. https:\/\/doi.org\/10.1101\/gr.236273.118","journal-title":"Genome Res"},{"issue":"4","key":"10281_CR19","doi-asserted-by":"publisher","first-page":"1265","DOI":"10.1093\/bioinformatics\/btz706","volume":"36","author":"M Marcet-Houben","year":"2020","unstructured":"Marcet-Houben M, Gabald\u00f3n T (2020) EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes. Bioinformatics 36(4):1265\u20131266. https:\/\/doi.org\/10.1093\/bioinformatics\/btz706","journal-title":"Bioinformatics"},{"issue":"1","key":"10281_CR20","doi-asserted-by":"publisher","first-page":"6327","DOI":"10.1038\/s41467-020-19777-8","volume":"11","author":"I Minkin","year":"2020","unstructured":"Minkin I, Medvedev P (2020) Scalable multiple whole-genome alignment and locally collinear block construction with Sibelia. Nat Commun 11(1):6327. https:\/\/doi.org\/10.1038\/s41467-020-19777-8. (number: 1 Publisher: Nature Publishing Group)","journal-title":"Nat Commun"},{"key":"10281_CR21","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.58542","volume":"9","author":"SJ Modlin","year":"2020","unstructured":"Modlin SJ, Conkle-Gutierrez D, Kim C et al (2020) Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife 9:e58542. https:\/\/doi.org\/10.7554\/eLife.58542","journal-title":"eLife"},{"issue":"5573","key":"10281_CR22","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1126\/science.1069193","volume":"296","author":"RJ Mural","year":"2002","unstructured":"Mural RJ, Adams MD, Myers EW et al (2002) A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296(5573):1661\u20131671. https:\/\/doi.org\/10.1126\/science.1069193","journal-title":"Science"},{"issue":"3","key":"10281_CR23","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1073\/pnas.81.3.814","volume":"81","author":"JH Nadeau","year":"1984","unstructured":"Nadeau JH, Taylor BA (1984) Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci USA 81(3):814\u2013818. https:\/\/doi.org\/10.1073\/pnas.81.3.814","journal-title":"Proc Natl Acad Sci USA"},{"key":"10281_CR24","unstructured":"Notredame C (2012) Robusta: a meta-multiple genome alignment tool. http:\/\/www.tcoffee.org\/Projects\/robusta"},{"issue":"1","key":"10281_CR25","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","volume":"17","author":"BD Ondov","year":"2016","unstructured":"Ondov BD, Treangen TJ, Melsted P et al (2016) Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17(1):132. https:\/\/doi.org\/10.1186\/s13059-016-0997-x","journal-title":"Genome Biol"},{"issue":"11","key":"10281_CR26","doi-asserted-by":"publisher","first-page":"1814","DOI":"10.1101\/gr.076554.108","volume":"18","author":"B Paten","year":"2008","unstructured":"Paten B, Herrero J, Beal K et al (2008) Enredo and pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 18(11):1814\u20131828. https:\/\/doi.org\/10.1101\/gr.076554.108","journal-title":"Genome Res"},{"issue":"1","key":"10281_CR27","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1101\/gr.757503","volume":"13","author":"P Pevzner","year":"2003","unstructured":"Pevzner P, Tesler G (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res 13(1):37\u201345. https:\/\/doi.org\/10.1101\/gr.757503","journal-title":"Genome Res"},{"issue":"6","key":"10281_CR28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2007-8-6-r124","volume":"8","author":"A Prakash","year":"2007","unstructured":"Prakash A, Tompa M (2007) Measuring the accuracy of genome-size multiple alignments. Genome Biol 8(6):1\u201311. https:\/\/doi.org\/10.1186\/gb-2007-8-6-r124","journal-title":"Genome Biol"},{"issue":"5","key":"10281_CR29","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1093\/genetics\/26.5.517","volume":"26","author":"AH Sturtevant","year":"1941","unstructured":"Sturtevant AH, Novitski E (1941) The homologies of the chromosome elements in the genus Drosophila. Genetics 26(5):517","journal-title":"Genetics"},{"key":"10281_CR30","doi-asserted-by":"publisher","first-page":"i21","DOI":"10.1093\/bioinformatics\/btaa503","volume":"36","author":"D Svetlitsky","year":"2020","unstructured":"Svetlitsky D, Dagan T, Ziv-Ukelson M (2020) Discovery of multi-operon colinear syntenic blocks in microbial genomes. Bioinformatics 36:i21\u2013i29. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa503","journal-title":"Bioinformatics"},{"issue":"6915","key":"10281_CR31","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/nature01262","volume":"420","author":"RH Waterston","year":"2002","unstructured":"Waterston RH, Lindblad-Toh K, Birney E et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520\u2013562. https:\/\/doi.org\/10.1038\/nature01262","journal-title":"Nature"},{"issue":"20","key":"10281_CR32","doi-asserted-by":"publisher","first-page":"9600","DOI":"10.1093\/nar\/gkw843","volume":"44","author":"S Winter","year":"2016","unstructured":"Winter S, Jahn K, Wehner S et al (2016) Finding approximate gene clusters with gecko 3. Nucleic Acids Res 44(20):9600\u20139610. https:\/\/doi.org\/10.1093\/nar\/gkw843","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Molecular Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-025-10281-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00239-025-10281-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00239-025-10281-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T01:03:04Z","timestamp":1767229384000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00239-025-10281-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":32,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["10281"],"URL":"https:\/\/doi.org\/10.1007\/s00239-025-10281-5","relation":{},"ISSN":["0022-2844","1432-1432"],"issn-type":[{"type":"print","value":"0022-2844"},{"type":"electronic","value":"1432-1432"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"16 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"There are no Conflict of interest to declare.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}