Software developed in the lab
4P - PARALLEL PROCESSING OF POLYMORPHISM PANELS
(authors: Andrea Benazzo, Alex Panziera and Giorgio Bertorelle)
4P is a software for computing basic population genetics statistics from large SNPs dataset.
The input data types handled by the program include ped/map, arp and vcf files.
The software allows the user to calculate the locus specific or the mean allele frequency, heterozygosity (expected and observed) and genetic distance between populations.
The genetic distance measurements included in this program are Nei’s Gst (1973), Nei’s Gst (1983), Hedrick’s G’st (2005), Jost’s D and Weir&Cockerham’s Fst (1984).
It also allows the computation of the single/joint allele frequency spectrum (folded/unfolded, using different dimensions) and the generation of a similarity/dissimilarity matrix between individuals.
4P is written in the C programming language using the OpenMP library to distribute computation among available CPU cores. This feature allows the program to make full use of the computational power of multi-core systems, allowing a significant reduction in computational times. 4P, being written in the fully compiled language C, is also able to handle datasets larger than the ones normally used in environments like R or with scripting languages (as Perl or Python).
System Requirements
Windows users needs to download and install the MinGW (http://www.mingw.org/) package before execute 4P binaries. This software provides essential windows libraries that are not included in 4P.
No particular system requirements are needed for Linux and Mac users. The software was tested on Ubuntu 12.04 (32 and 64 bit), Windows 7 (64 bit) and Mac OS X 10.6 Snow Leopard (32 and 64 bit).
Downloads
The source code, the manual and the precompiled binaries for Windows, Linux and MacOS can be downloaded at https://github.com/anbena/4p
Citation
NeON: an R package to estimate human effective population size and divergence time from patterns of linkage disequilibrium between SNPs
(authors: Massimo Mezzavilla and Silvia Ghirotto)
The NeON R package has been designed to explore population’s LD patterns in order to reconstruct two key parameters of human evolution: the effective population size and the divergence time between populations. NeON starts with binary or pairwise-LD PLINK files, and allows (a) to assign a genetic map position using HapMap (NCBI release 36 or 37) (b) to calculate the effective population size over time exploiting the relationship between Ne and the average squared correlation coefficient of LD (r2LD) within predefined recombination distance categories, and (c) to calculate the confidence interval about Ne based on the observed variation of the estimator across chromosomes. This package also offers the possibility to estimate the divergence time between populations given the Ne values calculated from the within-population LD data and a matrix of between-populations FST. These routines can easily be adapted to any species whenever genetic map positions are available.
System Requirements and Downloads
The package NeON, together with tutorial and examples, is available here for download and installation. It requires the package psych (http://CRAN.R-project.org/package=psych Version = 1.3.10) and the PLINK executable.
Citation
