{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:11Z","timestamp":1772138051767,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T00:00:00Z","timestamp":1655424000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Foundation","doi-asserted-by":"publisher","award":["STA 860\/6-2"],"award-info":[{"award-number":["STA 860\/6-2"]}],"id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]},{"name":"French Agence Nationale de la Recherche program (CoCoAlSeq project","award":["ANR-19-CE45-0012"],"award-info":[{"award-number":["ANR-19-CE45-0012"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Phylogenetic networks can represent non-treelike evolutionary scenarios. Current, actively developed approaches for phylogenetic network inference jointly account for non-treelike evolution and incomplete lineage sorting (ILS). Unfortunately, this induces a very high computational complexity and current tools can only analyze small datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present NetRAX, a tool for maximum likelihood (ML) inference of phylogenetic networks in the absence of ILS. Our tool leverages state-of-the-art methods for efficiently computing the phylogenetic likelihood function on trees, and extends them to phylogenetic networks via the notion of \u2018displayed trees\u2019. NetRAX can infer ML phylogenetic networks from partitioned multiple sequence alignments and returns the inferred networks in Extended Newick format. On simulated data, our results show a very low relative difference in Bayesian Information Criterion (BIC) score and a near-zero unrooted softwired cluster distance to the true, simulated networks. With NetRAX, a network inference on a partitioned alignment with 8000 sites, 30 taxa and 3 reticulations completes within a few minutes on a standard laptop.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Our implementation is available under the GNU General Public License v3.0 at https:\/\/github.com\/lutteropp\/NetRAX.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac396","type":"journal-article","created":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T09:38:06Z","timestamp":1655458686000},"page":"3725-3733","source":"Crossref","is-referenced-by-count":28,"title":["NetRAX: accurate and fast maximum likelihood phylogenetic network inference"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1300-5631","authenticated-orcid":false,"given":"Sarah","family":"Lutteropp","sequence":"first","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"}]},{"given":"C\u00e9line","family":"Scornavacca","sequence":"additional","affiliation":[{"name":"Institut des Sciences de l\u2019\u00c9volution Universit\u00e9 de Montpellier, CNRS, IRD, EPHE Place Eug\u00e8ne Bataillon , 34095 Montpellier Cedex 05, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7394-2718","authenticated-orcid":false,"given":"Alexey M","family":"Kozlov","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-4419","authenticated-orcid":false,"given":"Benoit","family":"Morel","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe 76128, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0353-0691","authenticated-orcid":false,"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies , Heidelberg 69118, Germany"},{"name":"Institute for Theoretical Informatics, Karlsruhe Institute of Technology , Karlsruhe 76128, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,6,17]]},"reference":[{"key":"2023041405344553100_","volume-title":"Estimating Phylogenetic Networks from Concatenated Sequence Alignments","author":"Allen-Savietta","year":"2020"},{"key":"2023041405344553100_","author":"An\u00e9","year":"2021"},{"key":"2023041405344553100_","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/sysbio\/syz056","article-title":"Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data","volume":"69","author":"Blair","year":"2019","journal-title":"Syst. 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