{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T11:13:45Z","timestamp":1775819625728,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions.<\/jats:p><jats:p>Availability: ape is distributed through the Comprehensive R Archive Network: http:\/\/cran.r-project.org\/web\/packages\/ape\/index.html Further information may be found at http:\/\/ape.mpl.ird.fr\/pegas\/<\/jats:p><jats:p>Contact: \u00a0Katharina.Huber@cmp.uea.ac.uk, Emmanuel.Paradis@ird.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts184","type":"journal-article","created":{"date-parts":[[2012,4,12]],"date-time":"2012-04-12T05:16:27Z","timestamp":1334207787000},"page":"1536-1537","source":"Crossref","is-referenced-by-count":273,"title":["ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R"],"prefix":"10.1093","volume":"28","author":[{"given":"Andrei-Alin","family":"Popescu","sequence":"first","affiliation":[{"name":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226\/5554 \u2013 UM2\/CNRS\/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"}]},{"given":"Katharina T.","family":"Huber","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226\/5554 \u2013 UM2\/CNRS\/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"}]},{"given":"Emmanuel","family":"Paradis","sequence":"additional","affiliation":[{"name":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226\/5554 \u2013 UM2\/CNRS\/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"}]}],"member":"286","published-online":{"date-parts":[[2012,4,11]]},"reference":[{"key":"2023012512310991600_B1","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S0893-9659(98)00148-7","article-title":"A polynomial time algorithm for constructing the refined Buneman tree","volume":"12","author":"Bryant","year":"1999","journal-title":"Appl. Math. 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