{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:42Z","timestamp":1787008482484,"version":"build-2736575974"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,3,16]],"date-time":"2018-03-16T00:00:00Z","timestamp":1521158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM101352"],"award-info":[{"award-number":["R01GM101352"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"name":"RAZ"},{"name":"RBRA"},{"DOI":"10.13039\/501100001853","name":"RAC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001853","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Arizona State University SOLUR"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Mutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifying mutations from MA lines. Here we describe accuMUlate, a probabilistic mutation caller that reflects the design of a typical MA experiment while being flexible enough to accommodate properties unique to any particular experiment.<\/jats:p>\n                    <jats:p>Availability and implementation accuMUlate is available from https:\/\/github.com\/dwinter\/accuMUlate.<\/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\/bty165","type":"journal-article","created":{"date-parts":[[2018,3,16]],"date-time":"2018-03-16T05:22:48Z","timestamp":1521177768000},"page":"2659-2660","source":"Crossref","is-referenced-by-count":18,"title":["accuMUlate: a mutation caller designed for mutation accumulation experiments"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6165-0029","authenticated-orcid":false,"given":"David J","family":"Winter","sequence":"first","affiliation":[{"name":"The Biodesign Institute, Arizona State University, Tempe, AZ, USA"},{"name":"Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven H","family":"Wu","sequence":"additional","affiliation":[{"name":"The Biodesign Institute, Arizona State University, Tempe, AZ, USA"},{"name":"Bioconsortia Inc, Davis, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail A","family":"Howell","sequence":"additional","affiliation":[{"name":"The Biodesign Institute, Arizona State University, Tempe, AZ, USA"},{"name":"School of Life Sciences, Arizona State University, Tempe, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ricardo B R","family":"Azevedo","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry, University of Houston, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca A","family":"Zufall","sequence":"additional","affiliation":[{"name":"Department of Biology and Biochemistry, University of Houston, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reed A","family":"Cartwright","sequence":"additional","affiliation":[{"name":"The Biodesign Institute, Arizona State University, Tempe, AZ, USA"},{"name":"School of Life Sciences, Arizona State University, Tempe, AZ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,16]]},"reference":[{"key":"2023012713083521400_bty165-B1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nature10555","article-title":"Spontaneous epigenetic variation in the Arabidopsis thaliana methylome","volume":"480","author":"Becker","year":"2011","journal-title":"Nature"},{"key":"2023012713083521400_bty165-B2","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1534\/genetics.116.193060","article-title":"The fitness effects of spontaneous mutations nearly unseen by selection in a bacterium with multiple chromosomes","volume":"204","author":"Dillon","year":"2016","journal-title":"Genetics"},{"key":"2023012713083521400_bty165-B3","doi-asserted-by":"crossref","first-page":"2843.","DOI":"10.1093\/bioinformatics\/btu356","article-title":"Toward better understanding of artifacts in variant calling from high-coverage samples","volume":"30","author":"Li","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713083521400_bty165-B4","first-page":"3629","article-title":"Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila","volume":"8","author":"Long","year":"2016","journal-title":"Genome Biol. 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