{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T04:31:38Z","timestamp":1775017898707,"version":"3.50.1"},"reference-count":48,"publisher":"World Scientific Pub Co Pte Ltd","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:p>Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.<\/jats:p>","DOI":"10.1142\/s0219720021400126","type":"journal-article","created":{"date-parts":[[2021,12,13]],"date-time":"2021-12-13T13:00:20Z","timestamp":1639400420000},"source":"Crossref","is-referenced-by-count":15,"title":["Comparing the topology of phylogenetic network generators"],"prefix":"10.1142","volume":"19","author":[{"given":"Remie","family":"Janssen","sequence":"first","affiliation":[{"name":"Delft University of Technology, Delft Institute of Applied Mathematics, Mekelweg 4, 2628 CD, Delft, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengyu","family":"Liu","sequence":"additional","affiliation":[{"name":"Simon Fraser University, Department of Mathematics, 8888 University Drive, Burnaby, BC V5A 1S6, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2021,12,6]]},"reference":[{"key":"S0219720021400126BIB001","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511974076"},{"key":"S0219720021400126BIB002","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-10837-3_13"},{"key":"S0219720021400126BIB003","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syz056"},{"key":"S0219720021400126BIB004","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2021.02.052"},{"key":"S0219720021400126BIB005","doi-asserted-by":"publisher","DOI":"10.1007\/s00285-015-0950-8"},{"key":"S0219720021400126BIB006","doi-asserted-by":"publisher","DOI":"10.1007\/s00285-018-1218-x"},{"key":"S0219720021400126BIB007","doi-asserted-by":"publisher","DOI":"10.1016\/j.aam.2020.102075"},{"key":"S0219720021400126BIB008","doi-asserted-by":"publisher","DOI":"10.1007\/s00285-005-0315-9"},{"key":"S0219720021400126BIB009","doi-asserted-by":"publisher","DOI":"10.1016\/j.aam.2019.01.004"},{"key":"S0219720021400126BIB010","doi-asserted-by":"publisher","DOI":"10.1137\/110845045"},{"key":"S0219720021400126BIB012","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2019.2934957"},{"key":"S0219720021400126BIB013","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx307"},{"key":"S0219720021400126BIB014","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005932"},{"issue":"10","key":"S0219720021400126BIB015","first-page":"1","volume":"16","author":"Yu Y","year":"2015","journal-title":"BMC Genom"},{"key":"S0219720021400126BIB016","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005896"},{"key":"S0219720021400126BIB017","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2009.22"},{"issue":"1","key":"S0219720021400126BIB018","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1109\/TCBB.2019.2895344","volume":"17","author":"Pons JC","year":"2019","journal-title":"IEEE\/ACM Trans Comput Biol Bioinf"},{"key":"S0219720021400126BIB019","first-page":"44","volume-title":"Advances in Applied Probability","author":"Harding EF","year":"1971"},{"key":"S0219720021400126BIB020","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl191"},{"key":"S0219720021400126BIB021","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2015.0228"},{"key":"S0219720021400126BIB022","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005611"},{"key":"S0219720021400126BIB024","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4612-0719-1_1"},{"key":"S0219720021400126BIB025","doi-asserted-by":"publisher","DOI":"10.1080\/10635150701884640"},{"key":"S0219720021400126BIB026","doi-asserted-by":"publisher","DOI":"10.1080\/10635150600889625"},{"key":"S0219720021400126BIB027","doi-asserted-by":"publisher","DOI":"10.1137\/1.9781611974485"},{"key":"S0219720021400126BIB029","doi-asserted-by":"publisher","DOI":"10.1016\/j.tpb.2020.02.001"},{"key":"S0219720021400126BIB031","doi-asserted-by":"publisher","DOI":"10.1016\/j.dam.2020.08.019"},{"key":"S0219720021400126BIB032","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2018.03.011"},{"key":"S0219720021400126BIB033","doi-asserted-by":"publisher","DOI":"10.1093\/comjnl\/9.1.60"},{"key":"S0219720021400126BIB034","volume-title":"Multidimensional Scaling","author":"Cox M","year":"2001"},{"key":"S0219720021400126BIB035","volume-title":"Finding Groups in Data: An Introduction to Cluster Analysis","author":"Kaufman L","year":"2009"},{"key":"S0219720021400126BIB036","doi-asserted-by":"publisher","DOI":"10.1016\/j.aim.2012.08.008"},{"key":"S0219720021400126BIB037","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2020.106781"},{"issue":"1","key":"S0219720021400126BIB038","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-20314-w","volume":"12","author":"Yang W","year":"2021","journal-title":"Nat Commun"},{"key":"S0219720021400126BIB039","volume-title":"Workshop, First EvoEvo Workshop, Satellite Workshop of ECAL2015","author":"Cuypers T","year":"2015"},{"key":"S0219720021400126BIB040","volume-title":"2nd EvoEvo Workshop, Satellite Workshop of CCS2016","author":"van Dijk B","year":"2016"},{"key":"S0219720021400126BIB041","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.56801"},{"key":"S0219720021400126BIB042","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006006"},{"key":"S0219720021400126BIB043","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2017.03.032"},{"issue":"3","key":"S0219720021400126BIB045","first-page":"266","volume":"39","author":"Shao KT","year":"1990","journal-title":"System Zool"},{"key":"S0219720021400126BIB046","doi-asserted-by":"publisher","DOI":"10.1007\/11415770_17"},{"key":"S0219720021400126BIB047","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syv037"},{"key":"S0219720021400126BIB048","doi-asserted-by":"publisher","DOI":"10.1016\/j.tcs.2020.12.031"},{"key":"S0219720021400126BIB049","doi-asserted-by":"publisher","DOI":"10.1016\/j.mbs.2019.04.009"},{"key":"S0219720021400126BIB050","doi-asserted-by":"publisher","DOI":"10.1007\/s11538-018-0463-x"},{"key":"S0219720021400126BIB051","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2007.70270"},{"key":"S0219720021400126BIB054","doi-asserted-by":"publisher","DOI":"10.1098\/rsos.160016"},{"key":"S0219720021400126BIB055","doi-asserted-by":"publisher","DOI":"10.1007\/s11538-018-0452-0"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720021400126","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T09:12:18Z","timestamp":1726305138000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720021400126"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12]]},"references-count":48,"journal-issue":{"issue":"06","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["10.1142\/S0219720021400126"],"URL":"https:\/\/doi.org\/10.1142\/s0219720021400126","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,12]]},"article-number":"2140012"}}