Estimating population diversity with CatchAll
Bunge, John, Woodard, Linda, Böhning, Dankmar, Foster, James, Connolly, Sean and Allen, Heather (2012) Estimating population diversity with CatchAll. Bioinfomatics, 28, (7), 1045-1047. (doi:10.1093/bioinformatics/bts075). (PMID:22333246).
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Description/Abstract
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.
| Item Type: | Article |
|---|---|
| ISSNs: | 1460-2059 (electronic) 1367-4803 (print) |
| Subjects: | H Social Sciences > HA Statistics Q Science > QA Mathematics Q Science > QH Natural history > QH301 Biology |
| Divisions: | Faculty of Medicine > Primary Care and Population Sciences Faculty of Social and Human Sciences > Mathematics > Statistics Faculty of Social and Human Sciences > Southampton Statistical Sciences Research Institute |
| Item ID: | 337593 |
| Date Deposited: | 30 Apr 2012 09:47 |
| Last Modified: | 26 Aug 2012 00:29 |
| Contributors: | Bunge, John (Author) Woodard, Linda (Author) Böhning, Dankmar (Author) Foster, James (Author) Connolly, Sean (Author) Allen, Heather (Author) , , |
| Date: | 15 March 2012 |
| Status: | Published |
| URI: | http://eprints.soton.ac.uk/id/eprint/337593 |
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