{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T13:53:46Z","timestamp":1776866026903,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The massive data produced by next-generation sequencing require advanced statistical tools. We address estimating the total diversity or species richness in a population. To date, only relatively simple methods have been implemented in available software. There is a need for software employing modern, computationally intensive statistical analyses including error, goodness-of-fit and robustness assessments.<\/jats:p>\n               <jats:p>Results: We present CatchAll, a fast, easy-to-use, platform-independent program that computes maximum likelihood estimates for finite-mixture models, weighted linear regression-based analyses and coverage-based non-parametric methods, along with outlier diagnostics. Given sample \u2018frequency count\u2019 data, CatchAll computes 12 different diversity estimates and applies a model-selection algorithm. CatchAll also derives discounted diversity estimates to adjust for possibly uncertain low-frequency counts. It is accompanied by an Excel-based graphics program.<\/jats:p>\n               <jats:p>Availability: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu\/catchall.<\/jats:p>\n               <jats:p>Contact: \u00a0jab18@cornell.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts075","type":"journal-article","created":{"date-parts":[[2012,2,15]],"date-time":"2012-02-15T01:50:26Z","timestamp":1329270626000},"page":"1045-1047","source":"Crossref","is-referenced-by-count":63,"title":["Estimating population diversity with CatchAll"],"prefix":"10.1093","volume":"28","author":[{"given":"John","family":"Bunge","sequence":"first","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Linda","family":"Woodard","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dankmar","family":"B\u00f6hning","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Foster","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sean","family":"Connolly","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heather K.","family":"Allen","sequence":"additional","affiliation":[{"name":"1 Department of Statistical Science, 2Center for Advanced Computing, Cornell University, Ithaca, NY 14853, USA, 3School of Mathematics, University of Southampton, Southampton SO17 1BJ, UK, 4Department of Biological Sciences, University of Idaho, Moscow, ID 83844, 5Charles River Associates, Boston, MA 02116 and 6Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, Ames, IA, 50010, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,2,13]]},"reference":[{"key":"2023012512220563900_B1","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00260-11","article-title":"Antibiotics in feed induce prophages in swine fecal microbiomes","volume":"2","author":"Allen","year":"2011","journal-title":"mBio"},{"key":"2023012512220563900_B2","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1111\/j.1462-2920.2010.02332.x","article-title":"Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions","volume":"13","author":"Behnke","year":"2011","journal-title":"Envrion. Microbiol."},{"key":"2023012512220563900_B3","article-title":"Estimating the number of species with CatchAll","volume-title":"Biocomputing 2011: Proceedings of the Pacific Symposium","author":"Bunge","year":"2011"},{"key":"2023012512220563900_B4","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1002\/bimj.200810452","article-title":"Parametric models for estimating the number of classes","volume":"50","author":"Bunge","year":"2008","journal-title":"Biometr. J."},{"key":"2023012512220563900_B5","article-title":"Estimating population diversity with unreliable low frequency counts","volume-title":"Biocomputing 2012: Proceedings of the Pacific Symposium","author":"Bunge","year":"2012"},{"key":"2023012512220563900_B6","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1080\/01621459.1992.10475194","article-title":"Estimating the number of classes via sample coverage","volume":"87","author":"Chao","year":"1992","journal-title":"J. Am. Stat. Associ."},{"key":"2023012512220563900_B7","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1214\/10-AOAS436","article-title":"Population size estimation based upon ratios of recapture probabilities","volume":"5","author":"Rocchetti","year":"2011","journal-title":"Ann. Appl. Stat."},{"key":"2023012512220563900_B8","doi-asserted-by":"crossref","first-page":"D546","DOI":"10.1093\/nar\/gkq1102","article-title":"Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource","volume":"39","author":"Sun","year":"2011","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/1045\/48879296\/bioinformatics_28_7_1045.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/7\/1045\/48879296\/bioinformatics_28_7_1045.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:48:12Z","timestamp":1674661692000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/7\/1045\/210529"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2,13]]},"references-count":8,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2012,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts075","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,4,1]]},"published":{"date-parts":[[2012,2,13]]}}}