{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T18:04:48Z","timestamp":1765994688933},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,3,28]],"date-time":"2020-03-28T00:00:00Z","timestamp":1585353600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>TNT (a widely used program for phylogenetic analysis) includes an interpreter for a scripting language, but that implementation is nonstandard and uses several conventions of its own. This article describes the implementation and basic usage of a C interpreter (with all the ISO essentials) now included in TNT. A phylogenetic library includes functions that can be used for manipulating trees and data, as well as other phylogeny-specific tasks. This greatly extends the capabilities of TNT.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Versions of TNT including the C interpreter for scripts can be downloaded from http:\/\/www.lillo.org.ar\/phylogeny\/tnt\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa214","type":"journal-article","created":{"date-parts":[[2020,3,25]],"date-time":"2020-03-25T12:10:20Z","timestamp":1585138220000},"page":"3988-3995","source":"Crossref","is-referenced-by-count":7,"title":["A phylogenetic C interpreter for TNT"],"prefix":"10.1093","volume":"36","author":[{"given":"Pablo A","family":"Goloboff","sequence":"first","affiliation":[{"name":"Unidad Ejecutora Lillo (Fundaci\u00f3n Miguel Lillo \u2013 Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas) , S. M. de Tucum\u00e1n 4000, Argentina"}]},{"given":"Mart\u00edn E","family":"Morales","sequence":"additional","affiliation":[{"name":"Unidad Ejecutora Lillo (Fundaci\u00f3n Miguel Lillo \u2013 Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas) , S. M. de Tucum\u00e1n 4000, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2020,3,28]]},"reference":[{"key":"2023062300444179200_btaa214-B1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/j.1096-0031.1994.tb00179.x","article-title":"Branch support and tree stability","volume":"10","author":"Bremer","year":"1994","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B2","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1504\/IJBRA.2009.026424","article-title":"An open source phylogenetic search and alignment package","volume":"5","author":"Carroll","year":"2009","journal-title":"Int. J. Bioinf. Res. App"},{"key":"2023062300444179200_btaa214-B3","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1007\/s11538-010-9579-3","article-title":"On the number of binary characters needed to recover a phylogeny using maximum parsimony","volume":"73","author":"Chai","year":"2011","journal-title":"Bull. Math. Biol"},{"key":"2023062300444179200_btaa214-B4","doi-asserted-by":"crossref","first-page":"50","DOI":"10.2307\/2412378","article-title":"On comparing the shapes of taxonomic trees","volume":"22","author":"Farris","year":"1973","journal-title":"Syst. Zool"},{"key":"2023062300444179200_btaa214-B5","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1093\/sysbio\/syu084","article-title":"The phylogenetic likelihood library","volume":"64","author":"Flouri","year":"2015","journal-title":"Syst. Biol"},{"key":"2023062300444179200_btaa214-B6","first-page":"1885","article-title":"Delayed-response phylogenetic correlation, an optimization-based method to test covariation of continuous characters","volume":"64","author":"Giannini","year":"2010","journal-title":"Evolution"},{"key":"2023062300444179200_btaa214-B7","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1111\/j.1096-0031.2007.00189.x","article-title":"Calculating SPR-distances between trees","volume":"24","author":"Goloboff","year":"2008","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B8","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.ympev.2014.06.008","article-title":"Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods","volume":"79","author":"Goloboff","year":"2014","journal-title":"Mol. Phyl. Evol"},{"key":"2023062300444179200_btaa214-B9","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1111\/cla.12380","article-title":"Likelihood approximations of implied weights parsimony can be selected over the Mk model by the Akaike information criterion","volume":"35","author":"Goloboff","year":"2019","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B10","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1111\/cla.12160","article-title":"TNT version 1.5, including a full implementation of geometric morphometrics","volume":"32","author":"Goloboff","year":"2016","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B11","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1111\/j.1096-0031.2002.tb00289.x","article-title":"Semi-Strict Supertrees","volume":"18","author":"Goloboff","year":"2002","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B12","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.ympev.2015.04.003","article-title":"Identifying unstable taxa: efficient implementation of triplet-based measures of stability, and comparison with Phyutility and RogueNaRok","volume":"88","author":"Goloboff","year":"2015","journal-title":"Mol. Phyl. Evol"},{"key":"2023062300444179200_btaa214-B13","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.ympev.2018.01.020","article-title":"On Defining a Unique Phylogenetic Tree with Homoplastic Characters","volume":"122","author":"Goloboff","year":"2018","journal-title":"Mol. Phyl. Evol"},{"key":"2023062300444179200_btaa214-B14","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1111\/j.1096-0031.2003.tb00376.x","article-title":"Improvements to resampling measures of group support","volume":"19","author":"Goloboff","year":"2003","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B15","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1111\/j.1096-0031.2008.00217.x","article-title":"TNT, a free program for phylogenetic analysis","volume":"24","author":"Goloboff","year":"2008","journal-title":"Cladistics"},{"key":"2023062300444179200_btaa214-B16","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1111\/zsc.12231","article-title":"Comparing tree-shapes: beyond symmetry","volume":"46","author":"Goloboff","year":"2017","journal-title":"Zool. Scripta"},{"key":"2023062300444179200_btaa214-B17","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1093\/sysbio\/syu039","article-title":"Probabilistic graphical model representation in phylogenetics","volume":"63","author":"H\u00f6hna","year":"2014","journal-title":"Syst. Biol"},{"key":"2023062300444179200_btaa214-B18","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1093\/sysbio\/syw021","article-title":"RevBayes: bayesian phylogenetic inference using graphical models and an interactive model-specification language","volume":"65","author":"H\u00f6hna","year":"2016","journal-title":"Syst. Biol"},{"key":"2023062300444179200_btaa214-B19","author":"Maddison","year":"2019"},{"key":"2023062300444179200_btaa214-B20","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"Robinson","year":"1981","journal-title":"Math. Biosc"},{"key":"2023062300444179200_btaa214-B21","author":"Saleeba","year":"2019"},{"key":"2023062300444179200_btaa214-B22","first-page":"163","volume-title":"Parsimony, Phylogeny, and Genomics","author":"Steel","year":"2005"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa214\/33400603\/btaa214.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/13\/3988\/50671446\/bioinformatics_36_13_3988.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/13\/3988\/50671446\/bioinformatics_36_13_3988.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T18:36:08Z","timestamp":1687631768000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/13\/3988\/5813334"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,3,28]]},"references-count":22,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2020,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa214","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2020,3,28]]}}}