Create README.md

README.md

@@ -0,0 +1,39 @@
+# PopLDdecay
+PopLDdecay: A new simple and efficient software for Linkage Disequilibrium Decay analysis based Variant Call Format
+
+
+
+1) Install
+        tar -zxvf  PopLDdecayXXX.tar.gz
+        cd PopLDdecayXXX;
+        cd src;
+        sh  make.sh
+        ../bin/PopLDdecay
+
+2) Example
+        1) Calculate LD decay
+        ./bin/PopLDdecay    -InVCF  SNP.vcf.gz  -OutStat LDdecay
+        2) draw the Figure
+        perl  bin/Plot_LDDecay.pl  -inFile   LDeecay.stat.gz  -output  Fig
+        3) you can see the  result  [LDeecay.stat.gz]  and   [Fig.png Fig.pdf]
+
+
+
+3) Introduction
+Linkage disequilibrium (LD) decay[1] is the most important and most common
+analysis in the population resequencing[2]. Special in the self-pollinated
+crops, the LD decay may not only reveal much about domestication and breed
+history[3], but also can reveal gene flow phenomenon, selection regions[1].
+However, to measure the LD decay, it takes too much resources and time by
+using currently existent software and tools. The LD decay studies also
+generate extraordinarily large amounts of data to temporary storage when you
+using the mainstream software "Haploview"[4], the classical LD
+processing tools. Effective use and analysis to get the LD decay result
+remains a difficult task for individual researchers. Here, we introduce
+PopLDdecay, a simple- efficient software for LD decay analysis, which
+processes the Variant Call Format (VCF)[5] file to produce the LD decay
+statistics results and plot the LD decay graphs. PopLDdecay is designed to use
+compressed data files as input or output to save storage space and it
+facilitates faster and more computationally efficient than the currently
+existent softwares. This software makes the LD decay pipeline significantly
+simplifies and user-friendly for the users.