title: Estimating population diversity with CatchAll.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Free executable downloads for Linux, Windows and Mac OS, with manual and source code, at www.northeastern.edu/catchall.
  
  
  BACKGROUND
  jab18@cornell.edu.
authors.affiliation: Department of Statistical Science, Cornell University, Ithaca, NY 14853, USA. jab18@cornell.edu
authors.forename: John
authors.initials: J
authors.lastname: Bunge
authors.forename: Linda
authors.initials: L
authors.lastname: Woodard
authors.forename: Dankmar
authors.initials: D
authors.lastname: Böhning
authors.forename: James A
authors.initials: JA
authors.lastname: Foster
authors.forename: Sean
authors.initials: S
authors.lastname: Connolly
authors.forename: Heather K
authors.initials: HK
authors.lastname: Allen
mesh_terms: D000465:Algorithms; D001435:Bacteriophages / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D005828:Genetics, Population / Q000379:methods* / Q000706:statistics & numerical data*; D016013:Likelihood Functions; D016014:Linear Models; D015233:Models, Statistical; D012984:Software