Estimating population diversity with CatchAll.

Bioinformatics
John BungeHeather K Allen

Abstract

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. 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 'frequency count' 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. Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. jab18@cornell.edu.

References

Dec 11, 2008·Biometrical Journal. Biometrische Zeitschrift·John Bunge, Kathryn Barger
Dec 1, 2011·MBio·Heather K AllenThaddeus B Stanton

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Citations

Mar 31, 2012·Annual Review of Marine Science·David A CaronAstrid Schnetzer
Jan 24, 2014·Microbiome·Heather K AllenThaddeus B Stanton
Oct 19, 2013·Science·Hans ter SteegeMiles R Silman
Nov 20, 2014·BMC Genomics·Daniel Aguirre de CárcerAntonio Alcamí
Jun 4, 2015·Biometrics·Amy Willis, John Bunge
Jul 20, 2013·Biometrics·Chang Xuan MaoJinhua Zhong
Sep 24, 2015·BMC Microbiology·Mackenzie Jonathan SlifierzJ Scott Weese
Jun 21, 2015·Applied Microbiology and Biotechnology·Charles H D WilliamsonJohn R Spear
Jun 20, 2015·Frontiers in Microbiology·Catherine M FebriaD Dudley Williams
Nov 17, 2015·Environmental Microbiology·Magdalena CalusinskaPhilippe Delfosse
Mar 29, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Shawn M D BearsonThaddeus B Stanton
Jun 9, 2016·FEMS Microbiology Ecology·Dominik ForsterThorsten Stoeck
Aug 4, 2016·BMC Research Notes·Heather K AllenThomas A Casey
Oct 23, 2012·Annals of Botany·Marjorie G Weber, Kathleen H Keeler
Apr 8, 2016·PloS One·Yiseul KimJoan B Rose
Apr 19, 2017·Ecology·Hans Ter SteegeRafael P Salomão
Oct 24, 2017·Science Advances·Anna TovoAmos Maritan
Jun 12, 2016·Applied and Environmental Microbiology·Emily A WalshSteven D'Hondt
Dec 19, 2015·BMC Bioinformatics·Duleepa JayasundaraSaman K Halgamuge
Feb 5, 2019·PLoS Biology·Stilianos LoucaLaura Wegener Parfrey
Feb 24, 2012·Environmental Microbiology·Charles Pepe-RanneyJohn R Spear
Feb 6, 2019·BMC Bioinformatics·Duleepa JayasundaraSaman K Halgamuge
Jul 18, 2017·Frontiers in Microbiology·Yiseul KimJoan B Rose
Aug 22, 2017·Frontiers in Microbiology·Jacob D HosenMargaret A Palmer
Aug 16, 2017·Nature Ecology & Evolution·Frédéric MahéMicah Dunthorn
Jun 24, 2020·BMC Genomics·Christina J CastroTerry Fei Fan Ng

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