{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:46:48Z","timestamp":1760784408317,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,2,28]],"date-time":"2018-02-28T00:00:00Z","timestamp":1519776000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["MC_U117573805","BB\/P007562\/1"],"award-info":[{"award-number":["MC_U117573805","BB\/P007562\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Existing ancestral sequence reconstruction techniques are ill-suited to investigating substitutions on a single branch of interest. We present SubRecon, an implementation of a hybrid technique integrating joint and marginal reconstruction for protein sequence data. SubRecon calculates the joint probability of states at adjacent internal nodes in a phylogeny, i.e. how the state has changed along a branch. This does not condition on states at other internal nodes and includes site rate variation. Simulation experiments show the technique to be accurate and powerful. SubRecon has a user-friendly command line interface and produces concise output that is intuitive yet suitable for subsequent parsing in an automated pipeline.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SubRecon is platform independent, requiring Java v1.8 or above. Source code, installation instructions and an example dataset are freely available under the Apache 2.0 license at https:\/\/github.com\/chrismonit\/SubRecon.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty101","type":"journal-article","created":{"date-parts":[[2018,2,27]],"date-time":"2018-02-27T12:17:36Z","timestamp":1519733856000},"page":"2297-2299","source":"Crossref","is-referenced-by-count":6,"title":["SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1717-0431","authenticated-orcid":false,"given":"Christopher","family":"Monit","sequence":"first","affiliation":[{"name":"Division of Infection and Immunity, University College London, London, UK"}]},{"given":"Richard A","family":"Goldstein","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, University College London, London, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,2,28]]},"reference":[{"key":"2023051604205359000_bty101-B1","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1093\/bioinformatics\/17.7.662","article-title":"PAL: an object-oriented programming library for molecular evolution and phylogenetics","volume":"17","author":"Drummond","year":"2001","journal-title":"Bioinformatics"},{"key":"2023051604205359000_bty101-B2","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. 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