{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T01:20:13Z","timestamp":1776388813647,"version":"3.51.2"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T00:00:00Z","timestamp":1592870400000},"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\/501100004837","name":"MICINN","doi-asserted-by":"publisher","award":["RTI2018-093336-B-C21"],"award-info":[{"award-number":["RTI2018-093336-B-C21"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010801","name":"Xunta de Galicia","doi-asserted-by":"publisher","award":["ED431G\/08"],"award-info":[{"award-number":["ED431G\/08"]}],"id":[{"id":"10.13039\/501100010801","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010801","name":"Xunta de Galicia","doi-asserted-by":"publisher","award":["ED431C-2018\/19"],"award-info":[{"award-number":["ED431C-2018\/19"]}],"id":[{"id":"10.13039\/501100010801","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>FastTree-2 is one of the most successful tools for inferring large phylogenies. With speed at the core of its design, there are still important issues in the FastTree-2 implementation that harm its performance and scalability. To deal with these limitations, we introduce VeryFastTree, a highly tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to boost performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>VeryFastTree is able to construct a tree on a standard server using double-precision arithmetic from an ultra-large 330k alignment in only 4.5\u2009h, which is 7.8\u00d7 and 3.5\u00d7 faster than the sequential and best parallel FastTree-2 times, respectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>VeryFastTree is available at the GitHub repository: https:\/\/github.com\/citiususc\/veryfasttree.<\/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\/btaa582","type":"journal-article","created":{"date-parts":[[2020,6,15]],"date-time":"2020-06-15T11:11:35Z","timestamp":1592219495000},"page":"4658-4659","source":"Crossref","is-referenced-by-count":77,"title":["Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6490-7128","authenticated-orcid":false,"given":"C\u00e9sar","family":"Pi\u00f1eiro","sequence":"first","affiliation":[{"name":"Centro de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela , Spain"}]},{"given":"Jos\u00e9 M","family":"Abu\u00edn","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9505-6493","authenticated-orcid":false,"given":"Juan C","family":"Pichel","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Tecnolox\u00edas Intelixentes (CiTIUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela , Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,6,23]]},"reference":[{"key":"2023062213564875900_btaa582-B1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst. 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