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Estimating population diversity with CatchAll.
Bunge, John; Woodard, Linda; Böhning, Dankmar; Foster, James A; Connolly, Sean; Allen, Heather K.
Afiliação
  • Bunge J; Department of Statistical Science, Cornell University, Ithaca, NY 14853, USA. jab18@cornell.edu
Bioinformatics ; 28(7): 1045-7, 2012 Apr 01.
Article em En | MEDLINE | ID: mdl-22333246
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. 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 '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. AVAILABILITY: Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall. CONTACT: jab18@cornell.edu.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Modelos Estatísticos / Genética Populacional Tipo de estudo: Guideline / Risk_factors_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2012 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Software / Modelos Estatísticos / Genética Populacional Tipo de estudo: Guideline / Risk_factors_studies Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2012 Tipo de documento: Article País de afiliação: Estados Unidos