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Matthew Dublin is a senior writer at Genome Technology. |
New Program Powers Population Diversity Research
May 23, 2012
Database designers at the Cornell University Center for Advanced Computing are providing researchers with a powerful new tool for exploring the microbial world.
Called "CatchAll," this program lives up to its name by computing 12 different diversity estimates with standard errors and goodness-of-fit assessments at various levels of outlier deletion. In instances wherein low-frequency counts may be false, CatchAll computes a discounted estimate by adjusting the diversity component of the selected mixture model.
"The massive data produced by sequencers require advanced statistical tools capable of accurately estimating the total diversity or 'species richness' in a microbial population," says John Bunge, an associate professor in Cornell's Department of Statistical Science.
The software is described in greater detail by Bunge and his colleagues in "Estimating population diversity with CatchAll," published in the journal Bioinformatics.
CatchAll has both command line and GUI interfaces and an associated Excel spreadsheet with graphical displays. Executable downloads for Linux, Windows, and Mac OS platforms with a manual and source code are available here.
