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Biol"},{"issue":"3","key":"pcbi.1010621.ref087","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1109\/TCBB.2018.2838667","article-title":"Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny","volume":"16","author":"L Urbini","year":"2019","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"pcbi.1010621.ref088","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1109\/TCBB.2013.22","article-title":"Unrooted Tree Reconciliation: A Unified Approach.","volume":"10","author":"P G\u00f3recki","year":"2013","journal-title":"IEEEACM Trans Comput Biol Bioinforma IEEE ACM"},{"issue":"18","key":"pcbi.1010621.ref089","doi-asserted-by":"crossref","first-page":"i409","DOI":"10.1093\/bioinformatics\/bts386","article-title":"Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees","volume":"28","author":"M Stolzer","year":"2012","journal-title":"Bioinformatics"},{"key":"pcbi.1010621.ref090","first-page":"12","article-title":"Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost.","author":"M Lafond","year":"2016"},{"issue":"18","key":"pcbi.1010621.ref091","doi-asserted-by":"crossref","first-page":"4822","DOI":"10.1093\/bioinformatics\/btaa615","article-title":"Treerecs: an integrated phylogenetic tool, from sequences to reconciliations","volume":"36","author":"N Comte","year":"2020","journal-title":"Bioinformatics"},{"key":"pcbi.1010621.ref092","first-page":"418","volume-title":"Reconciliation with Non-binary Gene Trees Revisited","author":"Y Zheng","year":"2014"},{"key":"pcbi.1010621.ref093","first-page":"187","volume-title":"On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees","author":"M Kordi","year":"2015"},{"key":"pcbi.1010621.ref094","first-page":"298","volume-title":"Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses.","author":"H Lai","year":"2017"},{"issue":"8","key":"pcbi.1010621.ref095","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1093\/bioinformatics\/btu806","article-title":"Improved gene tree error correction in the presence of horizontal gene transfer","volume":"31","author":"MS Bansal","year":"2015","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1010621.ref096","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1093\/molbev\/msh112","article-title":"A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process","volume":"21","author":"N Lartillot","year":"2004","journal-title":"Mol Biol Evol"},{"issue":"2","key":"pcbi.1010621.ref097","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":"B Boussau","year":"2013","journal-title":"Genome Res"},{"issue":"14","key":"pcbi.1010621.ref098","doi-asserted-by":"crossref","first-page":"5714","DOI":"10.1073\/pnas.0806251106","article-title":"Simultaneous Bayesian gene tree reconstruction and reconciliation analysis","volume":"106","author":"\u00d6 \u00c5kerborg","year":"2009","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"pcbi.1010621.ref099","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1748-7188-8-12","article-title":"Reconciliation and local gene tree rearrangement can be of mutual profit","volume":"8","author":"TH Nguyen","year":"2013","journal-title":"Algorithms Mol Biol"},{"key":"pcbi.1010621.ref100","first-page":"125","volume-title":"TreeSolve: Rapid Error-Correction of Microbial Gene Trees","author":"M Kordi","year":"2020"},{"issue":"3","key":"pcbi.1010621.ref101","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1093\/sysbio\/syu007","article-title":"A Bayesian Method for Analyzing Lateral Gene Transfer","volume":"63","author":"J Sj\u00f6strand","year":"2014","journal-title":"Syst Biol"},{"key":"pcbi.1010621.ref102","article-title":"Supertree Construction: Opportunities and Challenges.","author":"T. Warnow","year":"2018","journal-title":"ArXiv180503530 Q-Bio [Internet]."},{"key":"pcbi.1010621.ref103","first-page":"821439","article-title":"Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss.","author":"B Legried","year":"2020","journal-title":"bioRxiv"},{"key":"pcbi.1010621.ref104","first-page":"835553","article-title":"FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models.","author":"EK Molloy","year":"2020","journal-title":"bioRxiv"},{"issue":"1","key":"pcbi.1010621.ref105","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/1748-7188-8-28","article-title":"Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance","volume":"8","author":"R Chaudhary","year":"2013","journal-title":"Algorithms Mol Biol"},{"key":"pcbi.1010621.ref106","article-title":"Reconciliation of Gene and Species Trees With Polytomies.","author":"Y Zheng","year":"2012","journal-title":"ArXiv12013995 Q-Bio [Internet]."},{"issue":"2","key":"pcbi.1010621.ref107","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1006\/mpev.1996.0071","article-title":"Reconstruction of Ancient Molecular Phylogeny","volume":"6","author":"R Guigo","year":"1996","journal-title":"Mol Phylogenet Evol"},{"issue":"1","key":"pcbi.1010621.ref108","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1006\/mpev.1999.0676","article-title":"Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny","volume":"14","author":"RDM Page","year":"2000","journal-title":"Mol Phylogenet Evol"},{"issue":"3","key":"pcbi.1010621.ref109","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1137\/S0097539798343362","article-title":"From Gene Trees to Species Trees.","volume":"30","author":"B Ma","year":"2000","journal-title":"SIAM J Comput"},{"issue":"3","key":"pcbi.1010621.ref110","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1109\/TCBB.2010.74","article-title":"A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem","volume":"8","author":"MS Bansal","year":"2011","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"1","key":"pcbi.1010621.ref111","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1080\/10635150500354928","article-title":"Inferring phylogeny despite incomplete lineage sorting","volume":"55","author":"WP Maddison","year":"2006","journal-title":"Syst Biol"},{"issue":"1","key":"pcbi.1010621.ref112","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1471-2105-12-S1-S14","article-title":"An ILP solution for the gene duplication problem","volume":"12","author":"WC Chang","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"pcbi.1010621.ref113","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1093\/bioinformatics\/14.9.819","article-title":"GeneTree: comparing gene and species phylogenies using reconciled trees","volume":"14","author":"RD Page","year":"1998","journal-title":"Bioinformatics"},{"issue":"13","key":"pcbi.1010621.ref114","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/btn230","article-title":"DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony","volume":"24","author":"A Wehe","year":"2008","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1010621.ref115","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1186\/1471-2105-11-574","article-title":"iGTP: A software package for large-scale gene tree parsimony analysis","volume":"11","author":"R Chaudhary","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"9","key":"pcbi.1010621.ref116","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1093\/molbev\/msv115","article-title":"Species Tree Inference Using a Mixture Model","volume":"32","author":"I Ullah","year":"2015","journal-title":"Mol Biol Evol"},{"key":"pcbi.1010621.ref117","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1007\/s00026-004-0229-z","article-title":"On the Computational Complexity of the Rooted Subtree Prune and Regraft Distance.","volume":"8","author":"M Bordewich","year":"2005","journal-title":"Ann Comb"},{"issue":"2","key":"pcbi.1010621.ref118","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1007\/s10878-019-00396-z","article-title":"Gene tree reconciliation including transfers with replacement is hard and FPT","volume":"38","author":"D Hasic","year":"2019","journal-title":"J Comb Optim"},{"key":"pcbi.1010621.ref119","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1186\/1471-2105-11-324","article-title":"Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests","volume":"11","author":"SS Abby","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"pcbi.1010621.ref120","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/S0166-218X(96)00062-5","article-title":"On the complexity of comparing evolutionary trees","volume":"71","author":"J Hein","year":"1996","journal-title":"Discret Appl Math"},{"issue":"1","key":"pcbi.1010621.ref121","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.tcs.2006.12.011","article-title":"The maximum agreement forest problem: Approximation algorithms and computational experiments","volume":"374","author":"EM Rodrigues","year":"2007","journal-title":"Theor Comput Sci"},{"key":"pcbi.1010621.ref122","first-page":"514","volume-title":"On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation. 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Biol"},{"key":"pcbi.1010621.ref129","volume":"21","author":"B Rannala","journal-title":"Chapter 3.3 The Multi-species Coalescent Model and Species Tree Inference.:"},{"issue":"1","key":"pcbi.1010621.ref130","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13015-017-0098-8","article-title":"On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model","volume":"12","author":"D Bork","year":"2017","journal-title":"Algorithms Mol Biol"},{"key":"pcbi.1010621.ref131","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jtbi.2017.08.008","article-title":"Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations","volume":"432","author":"Y Chan","year":"2017","journal-title":"J Theor Biol"},{"key":"pcbi.1010621.ref132","first-page":"40","volume-title":"Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks.","author":"P Du","year":"2019"},{"issue":"4","key":"pcbi.1010621.ref133","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1101\/gr.123901.111","article-title":"Unified modeling of gene duplication, loss, and coalescence using a locus tree","volume":"22","author":"MD Rasmussen","year":"2012","journal-title":"Genome Res"},{"key":"pcbi.1010621.ref134","article-title":"Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees","author":"YC Wu","year":"2013","journal-title":"Genome Res"},{"issue":"2","key":"pcbi.1010621.ref135","doi-asserted-by":"crossref","first-page":"e00028","DOI":"10.1128\/mSystems.00028-16","article-title":"Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.","volume":"1","author":"KR Theis","year":"2016","journal-title":"mSystems"},{"key":"pcbi.1010621.ref136","first-page":"470","volume-title":"Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis.","author":"L Margulis","year":"1991"},{"issue":"8","key":"pcbi.1010621.ref137","doi-asserted-by":"crossref","first-page":"e1002226","DOI":"10.1371\/journal.pbio.1002226","article-title":"Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes","volume":"13","author":"SR Bordenstein","year":"2015","journal-title":"PLoS Biol"},{"issue":"5","key":"pcbi.1010621.ref138","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nrmicro1635","article-title":"The role of microorganisms in coral health, disease and evolution","volume":"5","author":"E Rosenberg","year":"2007","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"pcbi.1010621.ref139","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1111\/j.1574-6976.2008.00123.x","article-title":"Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution","volume":"32","author":"I Zilber-Rosenberg","year":"2008","journal-title":"FEMS Microbiol Rev"},{"key":"pcbi.1010621.ref140","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.genet.41.110306.130119","article-title":"Genomics and evolution of heritable bacterial symbionts","volume":"42","author":"NA Moran","year":"2008","journal-title":"Annu Rev Genet"},{"issue":"10","key":"pcbi.1010621.ref141","article-title":"Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer","volume":"8","author":"S L\u00f3pez-Madrigal","year":"2017","journal-title":"Genes [Internet]"},{"issue":"10","key":"pcbi.1010621.ref142","doi-asserted-by":"crossref","first-page":"e1003012","DOI":"10.1371\/journal.pgen.1003012","article-title":"Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii.","volume":"8","author":"T Penz","year":"2012","journal-title":"PLoS Genet"},{"issue":"28","key":"pcbi.1010621.ref143","doi-asserted-by":"crossref","first-page":"10257","DOI":"10.1073\/pnas.1409284111","article-title":"Evolutionary origin of insect\u2013Wolbachia nutritional mutualism","volume":"111","author":"N Nikoh","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010621.ref144","first-page":"1","article-title":"{i}n A, DSerial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids\u2019 di-symbiotic systems.","author":"AC acier","year":"2019","journal-title":"ISME J"},{"issue":"15","key":"pcbi.1010621.ref145","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1016\/j.cub.2013.06.027","article-title":"Defensive Bacteriome Symbiont with a Drastically Reduced Genome","volume":"23","author":"A Nakabachi","year":"2013","journal-title":"Curr Biol"},{"issue":"9","key":"pcbi.1010621.ref146","doi-asserted-by":"crossref","first-page":"2092","DOI":"10.1038\/ismej.2016.27","article-title":"Evidence of horizontal gene transfer between obligate leaf nodule symbionts","volume":"10","author":"M Pinto-Carb\u00f3","year":"2016","journal-title":"ISME J"},{"issue":"1","key":"pcbi.1010621.ref147","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-42227-5","article-title":"Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation","volume":"9","author":"H Jeong","year":"2019","journal-title":"Sci Rep"},{"issue":"7","key":"pcbi.1010621.ref148","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.pt.2013.05.001","article-title":"Hosts, parasites, and horizontal gene transfer","volume":"29","author":"BK Wijayawardena","year":"2013","journal-title":"Trends Parasitol"},{"issue":"5","key":"pcbi.1010621.ref149","doi-asserted-by":"crossref","first-page":"e1002693","DOI":"10.1371\/journal.ppat.1002693","article-title":"Age of the Association between Helicobacter pylori and Man","volume":"8","author":"Y Moodley","year":"2012","journal-title":"PLoS Pathog"},{"issue":"1836","key":"pcbi.1010621.ref150","doi-asserted-by":"crossref","first-page":"20160990","DOI":"10.1098\/rspb.2016.0990","article-title":"How old are bacterial pathogens?","volume":"283","author":"M. Achtman","year":"2016","journal-title":"Proc R Soc B Biol Sci"},{"key":"pcbi.1010621.ref151","article-title":"A Comprehensive Classification of Coronaviruses and Inferred Cross-Host Transmissions [Internet]","author":"Y Fu","year":"2020","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1010621.ref152","doi-asserted-by":"crossref","first-page":"150645","DOI":"10.1098\/rsos.150645","article-title":"Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales.","volume":"3","author":"SG da Silva","year":"2015","journal-title":"R Soc Open Sci"},{"issue":"1756","key":"pcbi.1010621.ref153","doi-asserted-by":"crossref","first-page":"20123065","DOI":"10.1098\/rspb.2012.3065","article-title":"Population structure and cultural geography of a folktale in Europe","volume":"280","author":"RM Ross","year":"2013","journal-title":"Proc R Soc B Biol Sci"},{"issue":"34","key":"pcbi.1010621.ref154","doi-asserted-by":"crossref","first-page":"9140","DOI":"10.1073\/pnas.1614395114","article-title":"Inferring patterns of folktale diffusion using genomic data","volume":"114","author":"E Bortolini","year":"2017","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi.1010621.ref155","article-title":"Ancient whole genome duplications and the evolution of the gene duplication and loss rate [Internet]","author":"A Zwaenepoel","year":"2019","journal-title":"Evol Biol"},{"key":"pcbi.1010621.ref156","first-page":"536","author":"RDM Page","year":"2001","journal-title":"Vertebrate phylogenomics: reconciled trees and gene duplications. In: Biocomputing 2002 [Internet]."},{"issue":"8","key":"pcbi.1010621.ref157","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1089\/cmb.2009.0139","article-title":"Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants.","volume":"16","author":"J g. Burleigh","year":"2009","journal-title":"J Comput Biol"},{"issue":"13","key":"pcbi.1010621.ref158","doi-asserted-by":"crossref","first-page":"i132","DOI":"10.1093\/bioinformatics\/btn150","article-title":"The multiple gene duplication problem revisited","volume":"24","author":"MS Bansal","year":"2008","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1010621.ref159","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13015-019-0139-6","article-title":"Reconciling multiple genes trees via segmental duplications and losses","volume":"14","author":"R Dondi","year":"2019","journal-title":"Algorithms Mol Biol"},{"issue":"5","key":"pcbi.1010621.ref160","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/gbe\/evx069","article-title":"DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies","volume":"9","author":"W Duchemin","year":"2017","journal-title":"Genome Biol Evol"},{"issue":"9","key":"pcbi.1010621.ref161","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1089\/cmb.2011.0066","article-title":"Detecting Highways of Horizontal Gene Transfer","volume":"18","author":"MS Bansal","year":"2011","journal-title":"J Comput Biol"},{"issue":"6","key":"pcbi.1010621.ref162","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1093\/molbev\/msab043","article-title":"Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes","volume":"38","author":"L Kloub","year":"2021","journal-title":"Mol Biol Evol"},{"key":"pcbi.1010621.ref163","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.jtbi.2017.01.024","article-title":"Fast algorithm for the reconciliation of gene trees and LGT networks","volume":"418","author":"C Scornavacca","year":"2017","journal-title":"J Theor Biol"},{"key":"pcbi.1010621.ref164","article-title":"Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting.","author":"Y Yu","year":"2012","journal-title":"ArXiv12121909 Cs Q-Bio [Internet]."},{"issue":"5","key":"pcbi.1010621.ref165","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1093\/sysbio\/syt037","article-title":"Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting","volume":"62","author":"Y Yu","year":"2013","journal-title":"Syst Biol"},{"key":"pcbi.1010621.ref166","first-page":"59","article-title":"The use of co-phylogeographic patterns to predict the nature of host\u2013parasite interactions, and vice versa.","author":"C Nieberding","year":"2010","journal-title":"In: The biogeography of host-parasite interactions."},{"issue":"7","key":"pcbi.1010621.ref167","doi-asserted-by":"crossref","first-page":"e101700","DOI":"10.1371\/journal.pone.0101700","article-title":"Do the Historical Biogeography and Evolutionary History of the Digenean Margotrema spp. across Central Mexico Mirror Those of Their Freshwater Fish Hosts (Goodeinae)?","volume":"9","author":"A Mart\u00ednez-Aquino","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"pcbi.1010621.ref168","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1080\/10635150490265085","article-title":"Biogeography Explains Cophylogenetic Patterns in Toucan Chewing Lice","volume":"53","author":"JD Weckstein","year":"2004","journal-title":"Syst Biol"},{"key":"pcbi.1010621.ref169","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.ympev.2017.03.003","article-title":"Cophylogenetics and biogeography reveal a coevolved relationship between sloths and their symbiont algae","volume":"110","author":"ED Fountain","year":"2017","journal-title":"Mol Phylogenet Evol"},{"issue":"5","key":"pcbi.1010621.ref170","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1111\/1755-0998.12897","article-title":"A geography-aware reconciliation method to investigate diversification patterns in host\/parasite interactions","volume":"18","author":"V Berry","year":"2018","journal-title":"Mol Ecol Resour"},{"issue":"2","key":"pcbi.1010621.ref171","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/molbev\/msr222","article-title":"Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny","volume":"29","author":"YC Wu","year":"2012","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pcbi.1010621.ref172","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1109\/TCBB.2018.2846253","article-title":"An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution.","volume":"16","author":"L Li","year":"2019","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"pcbi.1010621.ref173","doi-asserted-by":"crossref","unstructured":"Li L, Bansal MS. An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics [Internet]. New York, NY, USA: ACM; 2018 [cited 2019 Sep 25]. p. 386\u201397. (BCB \u201818). Available from: http:\/\/doi.acm.org\/10.1145\/3233547.3233603","DOI":"10.1145\/3233547.3233603"},{"key":"pcbi.1010621.ref174","first-page":"73","volume-title":"Simultaneous Multi-Domain-Multi-Gene Reconciliation Under the Domain-Gene-Species Reconciliation Model.","author":"L Li","year":"2019"},{"issue":"18","key":"pcbi.1010621.ref175","doi-asserted-by":"crossref","first-page":"3496","DOI":"10.1093\/bioinformatics\/btz081","article-title":"SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution","volume":"35","author":"S Kundu","year":"2019","journal-title":"Bioinformatics"},{"key":"pcbi.1010621.ref176","first-page":"336453","article-title":"Species tree-aware simultaneous reconstruction of gene and domain evolution","volume":"2","author":"SA Muhammad","year":"2018","journal-title":"bioRxiv"},{"issue":"5","key":"pcbi.1010621.ref177","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1093\/molbev\/msx073","article-title":"How Long Does Wolbachia Remain on Board?","volume":"34","author":"M Bailly-Bechet","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"12","key":"pcbi.1010621.ref178","doi-asserted-by":"crossref","first-page":"3082","DOI":"10.1111\/evo.12812","article-title":"Wing patterning genes and coevolution of M\u00fcllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times","volume":"69","author":"JFH Cuthill","year":"2015","journal-title":"Evolution"},{"issue":"1","key":"pcbi.1010621.ref179","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1093\/gbe\/evy272","article-title":"Toxin and Genome Evolution in a Drosophila Defensive Symbiosis","volume":"11","author":"MJ Ballinger","year":"2019","journal-title":"Genome Biol Evol"},{"issue":"6","key":"pcbi.1010621.ref180","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/sj.hdy.6801094","article-title":"Revisiting horizontal transfer of transposable elements in Drosophila","volume":"100","author":"ELS Loreto","year":"2008","journal-title":"Heredity"},{"issue":"7","key":"pcbi.1010621.ref181","doi-asserted-by":"crossref","first-page":"e3000390","DOI":"10.1371\/journal.pbio.3000390","article-title":"Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility","volume":"17","author":"R Denise","year":"2019","journal-title":"PLoS Biol"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010621","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T17:31:46Z","timestamp":1667496706000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010621"}},"subtitle":[],"editor":[{"given":"Daniel","family":"Mietchen","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,11,3]]},"references-count":181,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010621","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,3]]}}}