{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T20:44:21Z","timestamp":1769633061726,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,9]],"date-time":"2022-02-09T00:00:00Z","timestamp":1644364800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Agence Nationale pour la Recherche","award":["ANR-19-CE45-0010"],"award-info":[{"award-number":["ANR-19-CE45-0010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host\/symbiont to species\/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host\/symbiont\/gene complex.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/simonpenel\/thirdkind\/wiki.<\/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\/btac062","type":"journal-article","created":{"date-parts":[[2022,2,3]],"date-time":"2022-02-03T20:12:38Z","timestamp":1643919158000},"page":"2350-2352","source":"Crossref","is-referenced-by-count":23,"title":["Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1550-5477","authenticated-orcid":false,"given":"Simon","family":"Penel","sequence":"first","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive\/UMR5558, CNRS\/UCBL , Villeurbanne 69622, France"}]},{"given":"Hugo","family":"Menet","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive\/UMR5558, CNRS\/UCBL , Villeurbanne 69622, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4432-2680","authenticated-orcid":false,"given":"Th\u00e9o","family":"Tricou","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive\/UMR5558, CNRS\/UCBL , Villeurbanne 69622, France"}]},{"given":"Vincent","family":"Daubin","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive\/UMR5558, CNRS\/UCBL , Villeurbanne 69622, France"}]},{"given":"Eric","family":"Tannier","sequence":"additional","affiliation":[{"name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive\/UMR5558, CNRS\/UCBL , Villeurbanne 69622, France"},{"name":"Centre de Recherche Inria Lyon , Villeurbanne 69622, France"}]}],"member":"286","published-online":{"date-parts":[[2022,2,9]]},"reference":[{"key":"2023020109021343200_btac062-B1","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1089\/106652700750050871","article-title":"NOTUNG: a program for dating gene duplications and optimizing gene family trees","volume":"7","author":"Chen","year":"2000","journal-title":"J. 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