Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations.

Benazzo, A.; Panziera, A.; Bertorelle, G. (2015). 4P: Fast computing of population genetics statistics from large DNA polymorphism panels. ECOLOGY AND EVOLUTION, 5 (1): 172-175. doi: 10.1002/ece3.1261 handle: http://hdl.handle.net/10449/25065

4P: Fast computing of population genetics statistics from large DNA polymorphism panels

Panziera, Alex;
2015-01-01

Abstract

Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies. However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of data a very laborious task. Here, we present 4P (parallel processing of polymorphism panels), a stand-alone software program for the rapid computation of genetic variation statistics (including the joint frequency spectrum) from millions of DNA variants in multiple individuals and multiple populations. It handles a standard input file format commonly used to store DNA variation from empirical or simulation experiments. The computational performance of 4P was evaluated using large SNP (single nucleotide polymorphism) datasets from human genomes or obtained by simulations. 4P was faster or much faster than other comparable programs, and the impact of parallel computing using multicore computers or servers was evident. 4P is a useful tool for biologists who need a simple and rapid computer program to run exploratory population genetics analyses in large panels of genomic data. It is also particularly suitable to analyze multiple data sets produced in simulation studies. Unix, Windows, and MacOs versions are provided, as well as the source code for easier pipeline implementations.
Allelic spectrum
Fst
Genetic indicators
Genetic variation
NGS
Software
Settore BIO/11 - BIOLOGIA MOLECOLARE
Benazzo, A.; Panziera, A.; Bertorelle, G. (2015). 4P: Fast computing of population genetics statistics from large DNA polymorphism panels. ECOLOGY AND EVOLUTION, 5 (1): 172-175. doi: 10.1002/ece3.1261 handle: http://hdl.handle.net/10449/25065
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