{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:38:14Z","timestamp":1773272294972,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100016842","name":"Institut Fran\u00e7ais de Bioinformatique","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100016842","id-type":"DOI","asserted-by":"crossref"}]},{"name":"RENABI-IFB, Investissements d\u2019Avenir","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}]},{"name":"Agence Nationale pour la Recherche"},{"name":"GENOSPACE"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used to infer nucleotide, amino-acid or codon states at internal nodes of the tree, for every position along the sequence. These criteria generally select the state that maximizes (or minimizes) a given criterion. Although it is perfectly sensible from a statistical perspective, that strategy fails to convey useful information about the level of uncertainty associated to the inference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The present study introduces a new criterion for ancestral sequence reconstruction, the minimum posterior expected error (MPEE), that selects a single state whenever the signal conveyed by the data is strong, and a combination of multiple states otherwise. We also assess the performance of a criterion based on the Brier scoring scheme which, like MPEE, does not rely on any tuning parameters. The precision and accuracy of several other criteria that involve arbitrarily set tuning parameters are also evaluated. Large scale simulations demonstrate the benefits of using the MPEE and Brier-based criteria with a substantial increase in the accuracy of the inference of past sequences compared to the standard approach and realistic compromises on the precision of the solutions returned.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The software package PhyML (https:\/\/github.com\/stephaneguindon\/phyml) provides an implementation of the Maximum A Posteriori (MAP) and MPEE criteria for reconstructing ancestral nucleotide and amino-acid sequences.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz249","type":"journal-article","created":{"date-parts":[[2019,4,6]],"date-time":"2019-04-06T15:13:39Z","timestamp":1554563619000},"page":"4290-4297","source":"Crossref","is-referenced-by-count":14,"title":["Accounting for ambiguity in ancestral sequence reconstruction"],"prefix":"10.1093","volume":"35","author":[{"given":"A","family":"Oliva","sequence":"first","affiliation":[{"name":"Department of Computer Science, LIRMM, CNRS & Universit\u00e9 de Montpellier , Montpellier, France"},{"name":"Australian Centre for Ancient DNA , Adelaide, Australia"}]},{"given":"S","family":"Pulicani","sequence":"additional","affiliation":[{"name":"Department of Computer Science, LIRMM, CNRS & Universit\u00e9 de Montpellier , Montpellier, France"}]},{"given":"V","family":"Lefort","sequence":"additional","affiliation":[{"name":"Department of Computer Science, LIRMM, CNRS & Universit\u00e9 de Montpellier , Montpellier, France"}]},{"given":"L","family":"Br\u00e9h\u00e9lin","sequence":"additional","affiliation":[{"name":"Department of Computer Science, LIRMM, CNRS & Universit\u00e9 de Montpellier , Montpellier, France"}]},{"given":"O","family":"Gascuel","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Bioinformatique Evolutive, C3BI USR 3756, Institut Pasteur & CNRS , Paris, France"}]},{"given":"S","family":"Guindon","sequence":"additional","affiliation":[{"name":"Department of Computer Science, LIRMM, CNRS & Universit\u00e9 de Montpellier , Montpellier, France"}]}],"member":"286","published-online":{"date-parts":[[2019,4,12]]},"reference":[{"key":"2023062712473192700_btz249-B1","doi-asserted-by":"crossref","first-page":"W580","DOI":"10.1093\/nar\/gks498","article-title":"FastML: a web server for probabilistic reconstruction of ancestral sequences","volume":"40","author":"Ashkenazy","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023062712473192700_btz249-B2","doi-asserted-by":"crossref","first-page":"2701.","DOI":"10.1038\/s41598-017-02953-0","article-title":"Ancestral protein resurrection and engineering opportunities of the mamba aminergic toxins","volume":"7","author":"Blanchet","year":"2017","journal-title":"Scientific Rep"},{"key":"2023062712473192700_btz249-B3","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1126\/science.1123348","article-title":"Evolution of hormone-receptor complexity by molecular exploitation","volume":"312","author":"Bridgham","year":"2006","journal-title":"Science"},{"key":"2023062712473192700_btz249-B4","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0169-5347(99)01778-4","article-title":"Recreating ancestral proteins","volume":"15","author":"Chang","year":"2000","journal-title":"Trends Ecol. 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