AGDP: A software tool for the analysis of genome differences between populations

We developed a graphical program implementing statistical methods for genome-wide selection signature analysis, or more broadly defined as analysis of genome differences between populations. The analytical methods implemented include long-range allele frequency differences (AFD), standardized AFD, and long-range standardized heterozygosity of each population being compared in sliding windows of SNP markers. Collectively, the  standardized AFD and heterozygosity measures are referred to as ‘Z values’. AFD values for each chromosome are displayed on one Y-axis and Z values are displayed on the second Y-axis. All these measures are displayed in colored lines. The user may flip the two Y axes by clicking a button and may rescale the two Y axes to separate overlapping AFD and Z values by dragging a ‘ratio scale’. The graphical window can be re-sized to produce each figure in the size and shape the user prefers. The AGDP program has a separate calculation program for calculating the AFD and Z values by clicking one button of ‘run’. AFD and Z values for all chromosomes and multiple window sizes can be calculated by one ‘run’ and viewed by AGDP in scrolling and re-sizable graphical windows. Any or all graphs of publication quality for all chromosomes and window sizes can be saved by clicking one button. The AGDP program reduces a heavy data analysis task for studying population genome differences to a seamless data analysis process.