There are 8 files totally, include “Demo_script.R”, “FarmCPU_functions.txt”, “FarmCPU_help_document.pdf”, 
“gait_functions.txt”, “mdp_numeric.txt”, “mdp_SNP_information.txt”, “mdp_traits_validation.txt”, “README.txt”.


“Demo_script.R” is a demo script for a quick start of FarmCPU;

“FarmCPU_functions.txt” is FarmCPU source code;

“FarmCPU_help_document.pdf” is FarmCPU user manual;

“gait_functions.txt” is GAPIT (an R package) source code and FarmCPU use it for plot figures, this is also public available at: ‘http://zzlab.net/GAPIT/gapit_functions.txt';

“mdp_numeric.txt” is a genotype data for test;

“mdp_SNP_information.txt” is a SNP map information data for test;

“mdp_traits_validation.txt” is a phenotype data for test;

“README.txt” is a brief introduction of the files.


For “mdp_traits_validation.txt”, the first column is taxa name, from column 2 to column 5 are three real phenotypes: 
“EarHT”, “dpoll” and “EarDia”, last five columns are simulated traits with heritability of 0, 0.25, 0.05, 0.75 and 1.00. 
The coresponding QTNs are indicated below.

h2=0.25
SNP	Chromosome	Position
PZB02227.4	10	123742392
PZB01042.1	9	22041092
PZB02215.10	7	9142868
PZB00174.1	7	104898621
PZA00125.8	4	36047549
PZA03384.2	2	193285152
PZA02808.12	2	44606596
PZA00515.10	2	169265278
PZA00364.5	1	268082607
PZA01280.2	2	149428645

h2=50%
SNP	Chromosome	Position
PZA00579.6	9	147384958
PZB02534.2	8	128277210
PZA00705.5	1	95897171
PZA02479.1	4	218367682
PZA00495.4	2	170377910
PZA00363.6	3	132192142
Fea2.4	4	132736424
PZA00297.2	3	39992968
PZA03376.2	4	120655387
PZA00652.14	5	198380640

h2=75%
	QTN.position=c(1257,1973,	2676,	1754,	1533,	1644,	2232,	2663,	1045,	2286)# this can be used to plot dotted lines for QTNs in manhattan plot
SNP	Chromosome	Position
PZB01186.2	7	119650229
PZA03042.5	5	64413280
PZA03446.1	8	168485696
PZB00451.1	3	120915995
PZA00158.2	6	14057156
PZA03205.1	4	202883367
PZA03344.3	7	22002684
PZA03303.7	5	7648691
PHM3342.31	3	216028374
PZA01290.1	8	171827952

h2=100%
SNP	Chromosome	Position
PZA03675.2	7	61312392
PZA00069.4	5	214424975
PZA02808.12	2	44606596
PZA00527.10	2	216833071
PZA01946.7	7	123601837
PZA00947.1	9	96885738
PZA00096.26	7	144013500
PZA00498.5	8	48775713
PZA00702.5	3	185760526
PZA00663.5	4	141267246