{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T08:03:22Z","timestamp":1769846602741,"version":"3.49.0"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T00:00:00Z","timestamp":1704672000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T00:00:00Z","timestamp":1704672000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100017027","name":"State of Maryland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017027","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Algorithms Mol Biol"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in <jats:inline-formula><jats:alternatives><jats:tex-math>$$O(|\\Sigma |^{3.726}(n+k) + |\\Sigma |^{1.726}nk)$$<\/jats:tex-math><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                  <mml:mrow>\n                    <mml:mi>O<\/mml:mi>\n                    <mml:mo>(<\/mml:mo>\n                    <mml:mo>|<\/mml:mo>\n                    <mml:mi>\u03a3<\/mml:mi>\n                    <mml:msup>\n                      <mml:mo>|<\/mml:mo>\n                      <mml:mrow>\n                        <mml:mn>3.726<\/mml:mn>\n                      <\/mml:mrow>\n                    <\/mml:msup>\n                    <mml:mrow>\n                      <mml:mo>(<\/mml:mo>\n                      <mml:mi>n<\/mml:mi>\n                      <mml:mo>+<\/mml:mo>\n                      <mml:mi>k<\/mml:mi>\n                      <mml:mo>)<\/mml:mo>\n                    <\/mml:mrow>\n                    <mml:mo>+<\/mml:mo>\n                    <mml:mo>|<\/mml:mo>\n                    <mml:mi>\u03a3<\/mml:mi>\n                    <mml:msup>\n                      <mml:mo>|<\/mml:mo>\n                      <mml:mrow>\n                        <mml:mn>1.726<\/mml:mn>\n                      <\/mml:mrow>\n                    <\/mml:msup>\n                    <mml:mi>n<\/mml:mi>\n                    <mml:mi>k<\/mml:mi>\n                    <mml:mo>)<\/mml:mo>\n                  <\/mml:mrow>\n                <\/mml:math><\/jats:alternatives><\/jats:inline-formula> time, where <jats:italic>n<\/jats:italic> is the number of leaves, <jats:italic>k<\/jats:italic> is the number of characters, and <jats:inline-formula><jats:alternatives><jats:tex-math>$$\\Sigma$$<\/jats:tex-math><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                  <mml:mi>\u03a3<\/mml:mi>\n                <\/mml:math><\/jats:alternatives><\/jats:inline-formula> is the set of clades used as constraints. Dollo parsimony, which requires traits\/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence \/ absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.<\/jats:p>","DOI":"10.1186\/s13015-023-00249-9","type":"journal-article","created":{"date-parts":[[2024,1,8]],"date-time":"2024-01-08T18:03:06Z","timestamp":1704736986000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem"],"prefix":"10.1186","volume":"19","author":[{"given":"Junyan","family":"Dai","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tobias","family":"Rubel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunheng","family":"Han","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin K.","family":"Molloy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,1,8]]},"reference":[{"key":"249_CR1","doi-asserted-by":"publisher","unstructured":"Hallett MT, Lagergren J. New algorithms for the duplication-loss model. In: Proceedings of the Fourth Annual International Conference on Computational Molecular Biology. RECOMB \u201900, Association for Computing Machinery, New York, NY, USA 2000; pp. 138\u2013 146. https:\/\/doi.org\/10.1145\/332306.332359","DOI":"10.1145\/332306.332359"},{"key":"249_CR2","doi-asserted-by":"publisher","unstructured":"Bayzid MS, Warnow T. Gene Tree Parsimony for Incomplete Gene Trees. In: Schwartz, R., Reinert, K. (eds.) 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), vol. 88, Schloss Dagstuhl\u2013Leibniz-Zentrum fuer Informatik, Dagstuhl, Germany 2017; pp. 2\u2013 1213. https:\/\/doi.org\/10.4230\/LIPIcs.WABI.2017.2","DOI":"10.4230\/LIPIcs.WABI.2017.2"},{"key":"249_CR3","doi-asserted-by":"publisher","DOI":"10.1186\/s13015-017-0120-1","author":"MS Bayzid","year":"2018","unstructured":"Bayzid MS, Warnow T. Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms Mol Biol. 2018. https:\/\/doi.org\/10.1186\/s13015-017-0120-1.","journal-title":"Algorithms Mol Biol"},{"issue":"11","key":"249_CR4","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.1089\/cmb.2011.0174","volume":"18","author":"Y Yu","year":"2011","unstructured":"Yu Y, Warnow T, Nakhleh L. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. J Comput Biol. 2011;18(11):1543\u201359. https:\/\/doi.org\/10.1089\/cmb.2011.0174.","journal-title":"J Comput Biol"},{"issue":"1","key":"249_CR5","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1006\/jagm.2000.1133","volume":"38","author":"D Bryant","year":"2001","unstructured":"Bryant D, Steel M. Constructing optimal trees from quartets. J Algorithms. 2001;38(1):237\u201359. https:\/\/doi.org\/10.1006\/jagm.2000.1133.","journal-title":"J Algorithms"},{"issue":"17","key":"249_CR6","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1093\/bioinformatics\/btu462","volume":"30","author":"S Mirarab","year":"2014","unstructured":"Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics. 2014;30(17):541\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/btu462.","journal-title":"Bioinformatics"},{"issue":"11","key":"249_CR7","doi-asserted-by":"publisher","first-page":"3292","DOI":"10.1093\/molbev\/msaa139","volume":"37","author":"C Zhang","year":"2020","unstructured":"Zhang C, Scornavacca C, Molloy EK, Mirarab S. ASTRAL-Pro: Quartet-based species-tree inference despite paralogy. Mol Biol Evol. 2020;37(11):3292\u2013307. https:\/\/doi.org\/10.1093\/molbev\/msaa139.","journal-title":"Mol Biol Evol"},{"issue":"5","key":"249_CR8","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1093\/bioinformatics\/btw600","volume":"33","author":"P Vachaspati","year":"2016","unstructured":"Vachaspati P, Warnow T. FastRFS: fast and accurate robinson-foulds supertrees using constrained exact optimization. Bioinformatics. 2016;33(5):631\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btw600.","journal-title":"Bioinformatics"},{"key":"249_CR9","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1093\/bioinformatics\/btaa444","volume":"36","author":"EK Molloy","year":"2020","unstructured":"Molloy EK, Warnow T. FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinformatics. 2020;36:57\u201365. https:\/\/doi.org\/10.1093\/bioinformatics\/btaa444.","journal-title":"Bioinformatics"},{"issue":"12","key":"249_CR10","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1093\/bioinformatics\/btv234","volume":"31","author":"S Mirarab","year":"2015","unstructured":"Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics. 2015;31(12):44\u201352. https:\/\/doi.org\/10.1093\/bioinformatics\/btv234.","journal-title":"Bioinformatics"},{"issue":"6","key":"249_CR11","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s12859-018-2129-y","volume":"19","author":"C Zhang","year":"2018","unstructured":"Zhang C, Rabiee M, Sayyari E, Mirarab S. ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018;19(6):153. https:\/\/doi.org\/10.1186\/s12859-018-2129-y.","journal-title":"BMC Bioinformatics"},{"issue":"16","key":"249_CR12","doi-asserted-by":"publisher","first-page":"2317","DOI":"10.1093\/bioinformatics\/btab093","volume":"37","author":"P Dibaeinia","year":"2021","unstructured":"Dibaeinia P, Tabe-Bordbar S, Warnow T. FASTRAL: improving scalability of phylogenomic analysis. Bioinformatics. 2021;37(16):2317\u201324. https:\/\/doi.org\/10.1093\/bioinformatics\/btab093.","journal-title":"Bioinformatics"},{"key":"249_CR13","doi-asserted-by":"publisher","unstructured":"Bonizzoni P, Ciccolella S, Della\u00a0Vedova G, Soto M. Beyond perfect phylogeny: Multisample phylogeny reconstruction via ilp. In: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics. ACM-BCB \u201917, Association for Computing Machinery, New York, NY, USA 2017; pp. 1\u2013 10. https:\/\/doi.org\/10.1145\/3107411.3107441","DOI":"10.1145\/3107411.3107441"},{"issue":"5","key":"249_CR14","doi-asserted-by":"publisher","first-page":"1410","DOI":"10.1109\/TCBB.2018.2865729","volume":"16","author":"P Bonizzoni","year":"2019","unstructured":"Bonizzoni P, Ciccolella S, Vedova GD, Soto M. Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach. IEEE\/ACM Trans Comput Biol Bioinf. 2019;16(5):1410\u201323. https:\/\/doi.org\/10.1109\/TCBB.2018.2865729.","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"issue":"Suppl 1","key":"249_CR15","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1186\/s12859-020-03736-7","volume":"21","author":"S Ciccolella","year":"2020","unstructured":"Ciccolella S, Soto\u00a0Gomez M, Patterson M.D, Vedova G.D, Hajirasouliha I, Bonizzoni P. gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinformatics. 2020;21(Suppl 1):313. https:\/\/doi.org\/10.1186\/s12859-020-03736-7.","journal-title":"BMC Bioinformatics"},{"issue":"17","key":"249_CR16","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1093\/bioinformatics\/bty589","volume":"34","author":"M El-Kebir","year":"2018","unstructured":"El-Kebir M. SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. Bioinformatics. 2018;34(17):671\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/bty589.","journal-title":"Bioinformatics"},{"issue":"6","key":"249_CR17","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1093\/sysbio\/syz019","volume":"68","author":"A Cloutier","year":"2019","unstructured":"Cloutier A, Sackton TB, Grayson P, Clamp M, Baker AJ, Edwards SV. Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. Syst Biol. 2019;68(6):937\u201355. https:\/\/doi.org\/10.1093\/sysbio\/syz019.","journal-title":"Syst Biol"},{"key":"249_CR18","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1101\/gr.210948.116","volume":"27","author":"L Doronina","year":"2017","unstructured":"Doronina L, Churakov G, Kuritzin A, Shi J, Baertsch R, Clawson H, Schmitz J. Speciation network in laurasiatheria: retrophylogenomic signals. Genome Res. 2017;27:997\u20131003. https:\/\/doi.org\/10.1101\/gr.210948.116.","journal-title":"Genome Res"},{"issue":"5","key":"249_CR19","doi-asserted-by":"publisher","first-page":"766","DOI":"10.3390\/genes13050766","volume":"13","author":"L Doronina","year":"2022","unstructured":"Doronina L, Hughes GM, Moreno-Santillan D, Lawless C, Lonergan T, Ryan L, Jebb D, Kirilenko BM, Korstian JM, D\u00e1valos LM, Vernes SC, Myers EW, Teeling EC, Hiller M, Jermiin LS, Schmitz J, Springer MS, Ray DA. Contradictory phylogenetic signals in the laurasiatheria anomaly zone. Genes. 2022;13(5):766. https:\/\/doi.org\/10.3390\/genes13050766.","journal-title":"Genes"},{"key":"249_CR20","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s13100-018-0143-2","volume":"10","author":"F Lammers","year":"2019","unstructured":"Lammers F, Blumer M, R\u00fcckl\u00e9 C, Nilsson MA. Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation. Mob DNA. 2019;10:5. https:\/\/doi.org\/10.1186\/s13100-018-0143-2.","journal-title":"Mob DNA"},{"issue":"6","key":"249_CR21","doi-asserted-by":"publisher","first-page":"1664","DOI":"10.1093\/gbe\/evv099","volume":"7","author":"RN Platt","year":"2015","unstructured":"II RNP, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA. Targeted capture of phylogenetically informative VES sine insertions in genus myotis. Genome Biol Evol. 2015;7(6):1664\u201375. https:\/\/doi.org\/10.1093\/gbe\/evv099.","journal-title":"Genome Biol Evol"},{"issue":"3","key":"249_CR22","doi-asserted-by":"publisher","first-page":"399","DOI":"10.3390\/genes13030399","volume":"13","author":"JM Korstian","year":"2022","unstructured":"Korstian JM, Paulat NS, Platt RN II, Stevens RD, Ray DA. Sine-based phylogenomics reveal extensive introgression and incomplete lineage sorting in myotis. Genes. 2022;13(3):399. https:\/\/doi.org\/10.3390\/genes13030399.","journal-title":"Genes"},{"issue":"22","key":"249_CR23","doi-asserted-by":"publisher","first-page":"12787","DOI":"10.1073\/pnas.2133766100","volume":"100","author":"A-H Salem","year":"2003","unstructured":"Salem A-H, amd Jinchuan\u00a0Xing DAR, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. ALU elements and hominid phylogenetics. Proc Natl Acad Sci USA. 2003;100(22):12787\u201391. https:\/\/doi.org\/10.1073\/pnas.2133766100.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"249_CR24","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1186\/s12864-020-6519-y","volume":"21","author":"M Islam","year":"2020","unstructured":"Islam M, Sarker K, Das T, Reaz R, Bayzid MS. STELAR: a statistically consistent coalescent-based species tree estimation method by maximizing triplet consistency. BMC Genomics. 2020;21(1):136. https:\/\/doi.org\/10.1186\/s12864-020-6519-y.","journal-title":"BMC Genomics"},{"key":"249_CR25","doi-asserted-by":"publisher","DOI":"10.1017\/9781316882313","volume-title":"Computational Phylogenetics: an introduction to designing methods for phylogeny estimation","author":"T Warnow","year":"2017","unstructured":"Warnow T. Computational Phylogenetics: an introduction to designing methods for phylogeny estimation. Cambridge, United Kingdom: Cambridge University Press; 2017."},{"issue":"4","key":"249_CR26","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/sysbio\/20.4.406","volume":"20","author":"WM Fitch","year":"1971","unstructured":"Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol. 1971;20(4):406\u201316. https:\/\/doi.org\/10.1093\/sysbio\/20.4.406.","journal-title":"Syst Biol"},{"issue":"2","key":"249_CR27","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/0025-5564(82)90125-0","volume":"60","author":"RL Graham","year":"1982","unstructured":"Graham RL, Foulds LR. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Math Biosci. 1982;60(2):133\u201342. https:\/\/doi.org\/10.1016\/0025-5564(82)90125-0.","journal-title":"Math Biosci"},{"key":"249_CR28","doi-asserted-by":"publisher","DOI":"10.1016\/j.aam.2021.102252","volume":"131","author":"R Bouckaert","year":"2021","unstructured":"Bouckaert R, Fischer M, Wicke K. Combinatorial perspectives on Dollo-k characters in phylogenetics. Adv Appl Math. 2021;131: 102252. https:\/\/doi.org\/10.1016\/j.aam.2021.102252.","journal-title":"Adv Appl Math"},{"issue":"1","key":"249_CR29","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0025-5564(86)90161-6","volume":"81","author":"WHE Day","year":"1986","unstructured":"Day WHE, Johnson DS, Sankoff D. The computational complexity of inferring rooted phylogenies by parsimony. Math Biosci. 1986;81(1):33\u201342. https:\/\/doi.org\/10.1016\/0025-5564(86)90161-6.","journal-title":"Math Biosci"},{"key":"249_CR30","unstructured":"Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts 2003"},{"key":"249_CR31","unstructured":"Felsenstein J. PHYLIP (Phylogeny Inference Package). https:\/\/evolution.genetics.washington.edu\/phylip.html. Accessed 2005."},{"key":"249_CR32","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1146\/annurev.es.14.110183.001525","volume":"14","author":"J Felsenstein","year":"1983","unstructured":"Felsenstein J. Parsimony in systematics: biological and statistical issues. Ann Rev Ecol Syst. 1983;14:313\u201333.","journal-title":"Ann Rev Ecol Syst"},{"key":"249_CR33","doi-asserted-by":"publisher","unstructured":"Felsenstein J. Inferring phylogenies, 2nd edn. Sinauer Associates, Inc., Sunderland, Massachusetts 2004;. https:\/\/doi.org\/10.1007\/BF01734359","DOI":"10.1007\/BF01734359"},{"key":"249_CR34","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1007\/BF01681346","volume":"9","author":"D Sankoff","year":"1975","unstructured":"Sankoff D, Rousseau P. Locating the vertices of a Steiner tree in an arbitrary metric space. Math Program. 1975;9:240\u20136. https:\/\/doi.org\/10.1007\/BF01681346.","journal-title":"Math Program"},{"key":"249_CR35","doi-asserted-by":"publisher","unstructured":"Kane D, Tao T. A bound on partitioning clusters. Electron J Combinatorics 2017; https:\/\/doi.org\/10.37236\/6797","DOI":"10.37236\/6797"},{"key":"249_CR36","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1017\/S0370164600023993","volume":"42","author":"RA Fisher","year":"1923","unstructured":"Fisher RA. On the dominance ratio. Proc R Soc Edinb. 1923;42:321\u201341. https:\/\/doi.org\/10.1017\/S0370164600023993.","journal-title":"Proc R Soc Edinb"},{"issue":"2","key":"249_CR37","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1093\/genetics\/16.2.97","volume":"16","author":"S Wright","year":"1931","unstructured":"Wright S. Evolution in mendelian populations. Genetics. 1931;16(2):97\u2013159. https:\/\/doi.org\/10.1093\/genetics\/16.2.97.","journal-title":"Genetics"},{"key":"249_CR38","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s10577-017-9570-z","volume":"26","author":"RN Platt","year":"2018","unstructured":"Platt RN, Vandewege MW, Ray DA. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res. 2018;26:25\u201343. https:\/\/doi.org\/10.1007\/s10577-017-9570-z.","journal-title":"Chromosome Res"},{"key":"249_CR39","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1080\/106351500750049851","volume":"49","author":"AM Shedlock","year":"2000","unstructured":"Shedlock AM, Milinkovitch MC, Okada N. SINE evolution, missing data, and the origin of whales. Syst Biol. 2000;49:808\u201317.","journal-title":"Syst Biol"},{"key":"249_CR40","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2148-10-302","volume":"10","author":"L Liu","year":"2010","unstructured":"Liu L, Yu L, Edwards SV. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol. 2010;10:302. https:\/\/doi.org\/10.1186\/1471-2148-10-302.","journal-title":"BMC Evol Biol"},{"issue":"9","key":"249_CR41","doi-asserted-by":"publisher","first-page":"1830","DOI":"10.3390\/genes14091830","volume":"14","author":"L Doronina","year":"2023","unstructured":"Doronina L, Ogoniak L, Schmitz J. Homoplasy of retrotransposon insertions in toothed whales. Genes. 2023;14(9):1830. https:\/\/doi.org\/10.3390\/genes14091830.","journal-title":"Genes"},{"issue":"2","key":"249_CR42","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","volume":"18","author":"RR Hudson","year":"2002","unstructured":"Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002;18(2):337\u20138. https:\/\/doi.org\/10.1093\/bioinformatics\/18.2.337.","journal-title":"Bioinformatics"},{"issue":"3","key":"249_CR43","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1093\/sysbio\/syab086","volume":"71","author":"EK Molloy","year":"2021","unstructured":"Molloy EK, Gatesy J, Springer MS. Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone. Syst Biol. 2021;71(3):721\u201340. https:\/\/doi.org\/10.1093\/sysbio\/syab086.","journal-title":"Syst Biol"},{"issue":"2","key":"249_CR44","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1093\/sysbio\/syv082","volume":"65","author":"D Mallo","year":"2015","unstructured":"Mallo D, De Oliveira Martins L, Posada D. SimPhy\u202f: phylogenomic simulation of gene, locus, and species trees. Syst Biol. 2015;65(2):334\u201344. https:\/\/doi.org\/10.1093\/sysbio\/syv082.","journal-title":"Syst Biol"},{"issue":"2","key":"249_CR45","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1093\/jhered\/esz076","volume":"111","author":"MS Springer","year":"2019","unstructured":"Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-aware analysis of low-homoplasy retroelement insertions: Inference of species trees and introgression using quartets. J Hered. 2019;111(2):147\u201368. https:\/\/doi.org\/10.1093\/jhered\/esz076.","journal-title":"J Hered"},{"issue":"20","key":"249_CR46","doi-asserted-by":"publisher","first-page":"3961","DOI":"10.1093\/bioinformatics\/btz211","volume":"35","author":"J Yin","year":"2019","unstructured":"Yin J, Zhang C, Mirarab S. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics. 2019;35(20):3961\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btz211.","journal-title":"Bioinformatics"},{"key":"249_CR47","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1186\/s12864-018-4621-1","volume":"19","author":"P Vachaspati","year":"2018","unstructured":"Vachaspati P, Warnow T. SIESTA: enhancing searches for optimal supertrees and species trees. BMC Genom. 2018;19:252. https:\/\/doi.org\/10.1186\/s12864-018-4621-1.","journal-title":"BMC Genom"}],"container-title":["Algorithms for Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13015-023-00249-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13015-023-00249-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13015-023-00249-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T06:04:09Z","timestamp":1704780249000},"score":1,"resource":{"primary":{"URL":"https:\/\/almob.biomedcentral.com\/articles\/10.1186\/s13015-023-00249-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,8]]},"references-count":47,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["249"],"URL":"https:\/\/doi.org\/10.1186\/s13015-023-00249-9","relation":{},"ISSN":["1748-7188"],"issn-type":[{"value":"1748-7188","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1,8]]},"assertion":[{"value":"18 October 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 December 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 January 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no compng interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"2"}}