{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T03:53:36Z","timestamp":1769313216537,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,3,6]],"date-time":"2019-03-06T00:00:00Z","timestamp":1551830400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Rutherford Foundation Postdoctoral Fellowship"},{"DOI":"10.13039\/501100001509","name":"Royal Society of New Zealand","doi-asserted-by":"publisher","award":["RFT-VUW1501-PD"],"award-info":[{"award-number":["RFT-VUW1501-PD"]}],"id":[{"id":"10.13039\/501100001509","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Hidden Markov models (HMMs) and profile HMMs form an integral part of biological sequence analysis, supporting an ever-growing list of applications. The aphid R package can be used to derive, train, plot, import and export HMMs and profile HMMs in the R environment. Computationally-intensive dynamic programing recursions, such as the Viterbi, forward and backward algorithms are implemented in C++ and parallelized for increased speed and efficiency.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The aphid package is released under the GPL-3 license, and is freely available for download from CRAN and GitHub (https:\/\/github.com\/shaunpwilkinson\/aphid).<\/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\/btz159","type":"journal-article","created":{"date-parts":[[2019,3,2]],"date-time":"2019-03-02T12:09:39Z","timestamp":1551528579000},"page":"3829-3830","source":"Crossref","is-referenced-by-count":20,"title":["aphid: an R package for analysis with profile hidden Markov models"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7332-7931","authenticated-orcid":false,"given":"Shaun P","family":"Wilkinson","sequence":"first","affiliation":[{"name":"School of Biological Sciences, Victoria University of Wellington , Wellington, New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2019,3,6]]},"reference":[{"key":"2023013108193061600_btz159-B1","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","volume-title":"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids","author":"Durbin","year":"1998"},{"key":"2023013108193061600_btz159-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i08","article-title":"Rcpp: seamless R and C++ integration","volume":"40","author":"Eddelbuettel","year":"2011","journal-title":"J. Stat. Softw"},{"key":"2023013108193061600_btz159-B3","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1038\/nbt1004-1315","article-title":"What is a hidden Markov model?","volume":"22","author":"Eddy","year":"2004","journal-title":"Nat. Biotechnol"},{"key":"2023013108193061600_btz159-B4","first-page":"205","article-title":"A new generation of homology search tools based on probabilistic inference","volume":"23","author":"Eddy","year":"2009","journal-title":"Gen. Inform"},{"key":"2023013108193061600_btz159-B5","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1006\/jmbi.1994.1104","article-title":"Hidden Markov models in computational biology: applications to protein modeling","volume":"235","author":"Krogh","year":"1994","journal-title":"J. Mol. Biol"},{"key":"2023013108193061600_btz159-B6","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"2023013108193061600_btz159-B7","volume-title":"R: A Language and Environment for Statistical Computing","year":"2018"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/19\/3829\/48977331\/bioinformatics_35_19_3829.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/19\/3829\/48977331\/bioinformatics_35_19_3829.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T15:04:52Z","timestamp":1675177492000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/19\/3829\/5370175"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,3,6]]},"references-count":7,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2019,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz159","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,10,1]]},"published":{"date-parts":[[2019,3,6]]}}}