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4P - Parallel Processing of Polymorphism Panels
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4P (Parallel Processing of Polymorphism Panels) is a software for computing 
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 allele frequencies, the mean and
locus by locus heterozygosities (expected and observed), and several measures 
of genetic distance between populations (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 and joint allele frequency spectrum
(folded and unfolded, using different dimensions) and the matrix of similarity 
and dissimilarity indices (based on allele sharing) 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 able to handle datasets larger than 
those used in environments like R or with scripting languages (as Perl or Python).

Package content:
/src: the source code folder
/bin: 32-64 bit binaries for win/mac/linux
/doc: manual pdf
/examples: example files
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Basic usage:
1- set proper statistics in the sumstat.par file (all statistics are switched off by default)
2- type "4P_<bit>_<platform> -h" for an overview over the basic options
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Some usage examples:
example run:	4P -f example_20ind_10snp.ped -m example_20ind_10snp.map -i 0 -n 20 -s 10 -t 1
example run:	4P -f example_1000ind_100snp.arp -i 1 -n 1000 -s 100 -t 2
example run:	4P -f example_10ind_10snp.vcf -i 2 -n 10 -s 10 -t 1 -p example_pop_index.txt
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Compiling informations:
enter the src directory and type 
compile linux:	gcc -O3 -fopenmp -lm -D_FILE_OFFSET_BITS=64 -o 4P ./*.c
compile mac:	gcc -O3 -fopenmp -lm -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=0 -mmacosx-version-min=10.6 -o 4p_mac ./*.c
compile win:	see manual
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