Update README.md

README.md

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 # VCF2Dis
+<b>VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format</b>
+
+###  1) Install
+------------
+
+<b> [Download](https://github.com/BGI-shenzhen/VCF2Dis/archive/v1.36.tar.gz) </b>
+
+
+  </br> Just [make]  or [sh  make.sh ]  to compile this software.the final software can be found in the Dir <b>[bin/VCF2Dis]</b>
+  </br> For <b>linux /Unix </b> and <b>macOS</b>
+  <pre>
+        tar -zxvf  VCF2DisXXX.tar.gz             # if Link do not work ,Try <b>re-install</b> [zlib]library
+        cd VCF2DisXXX;                           # [zlib] and copy them to the library Dir
+        make ; make clean                        # VCF2Dis-xx/src/include/zlib
+        ./bin/VCF2Dis
+  </pre>
+
+**Note:** If fail to link,try to <b>re-install</b> the libraries [**_zlib_**](https://zlib.net/)
+
+###  2) an Example of nj-tree with no boostrap 
+------------
+* 1) Parameter description:
+```php
+	Usage: VCF2Dis -InPut  <in.vcf>  -OutPut  <p_dis.mat>
+
+		-InPut     <str>     Input one or muti GATK VCF genotype File
+		-OutPut    <str>     OutPut Sample p-Distance matrix
+
+		-InList    <str>     Input GATK muti-chr VCF Path List
+		-SubPop    <str>     SubGroup SampleList of VCFFile [ALLsample]
+		-Rand      <float>   Probability (0-1] for each site to join Calculation [1]
+		-KeepMF              Keep the Middle File diff & Use matrix
+
+		-help                Show more help [hewm2008 v1.36]
+
+```
+
+* 2) To Create the  p_distance matrix
+
+```
+# 2.1) To new all the sample p_distance matrix based VCF, run VCF2Dis directly
+      ./bin/VCF2Dis	-InPut	in.vcf.gz	-OutPut p_dis.mat
+
+# 2.2) To new sub group sample p_distance matrix ; put their sample name into File sample.list
+      ./bin/VCF2Dis	-InPut	chr1.vcf.gz chr2.vcf.gz	-OutPut p_dis.mat  -SubPop  sample.list
+```
+
+* 3) construct nj-tree and present it (need deal with Other software)
+```
+      #    3.1 Run  PHYLIP  
+      #   After p_distance done , software PHYLIP 3.69 (http://evolution.genetics.washington.edu/phylip.html) ,with neighbor-joining method can was used to construct the phylogenetic tree on the basis of this  p_distance matrix;
+       
+           PHYLIPNEW-3.69.650/bin/fneighbor  -datafile p_dis.matrix  -outfile tree.out1.txt -matrixtype s -treetype n -outtreefile tree.out2.tre
+
+      #    3.2 Run  MEGA  
+      #    The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file [tree.out2.tre]	
+```
+* 4) you can see the neighbor-joining tree and save it as PDF format
+
+
+###  3) an Example of nj-tree with boostrap 
+
+* 1) muti-run the nj-tree by using  put back sampling.
+To using the the part of the sites and new the nj-tree as above. Repeat For the <b>NN</b> times. X=(1,2....NN);
+
+```
+    ./bin/VCF2Dis	-InPut	in.vcf.gz	-OutPut p_dis_X.mat    -Rand     0.25
+    PHYLIPNEW-3.69.650/bin/fneighbor  -datafile p_dis_X.matrix  -outfile tree.out1_X.txt -matrixtype s -treetype n -outtreefile tree.out2_X.tre 
+```
+
+* 2) merge the all the  put back sampling  NJ-tree and construct  boostrap nj-tree.
+
+```
+	cat   tree.out2_*.tre   >  ALLtree_merge.tre
+	PHYLIPNEW-3.69.650/bin/fconsense   -intreefile   ALLtree_merge.tre  -outfile out  -treeprint Y
+	perl  ./bin/percentageboostrapTree.pl    ALLtree_merge.treefile    NN    Final_boostrap.tre
+```
+* 3) construct nj-tree and present it (need deal with Other software)
+```
+      #    The MEGA6 (http://www.megasoftware.net/) was used to present the phylogenetic tree based this file Final_boostrap.tre] 
+```
+------------
+###  4) Introduction
+------------
+To new the p_distance matrix besed the VCF file. the more infomation about the p_distance matrix, see [this website.](http://evolution.genetics.washington.edu/phylip/doc/distance.html)
+The VCF SNPs datasets were used to calculate p-distance between individuals, according to the follow formula to operate the sample i and sample j genetic distance:
+
+                D_ij=(1/L) * [(sum(d(l)_ij))]
+
+  </br> Where L is the length of regions where SNPs can be identified, and given the alleles at position l are A/C:
+```
+            d(l)_ij=0.0     if the genotypes of the two individuals were AA and AA;
+            d(l)_ij=0.5     if the genotypes of the two individuals were AA and AC;
+            d(l)_ij=0.0     if the genotypes of the two individuals were AC and AC;
+            d(l)_ij=1.0     if the genotypes of the two individuals were AA and CC;
+            d(l)_ij=0.0     if the genotypes of the two individuals were CC and CC;
+```
+
+
+
+###  5) Results
+------------
+some NJ-tree images which I draw in the paper before.
+
+* [50 Rices NBT](http://www.nature.com/nbt/journal/v30/n1/images/nbt.2050-F1.jpg)
+* [31 soybeans  NG]( http://www.nature.com/ng/journal/v42/n12/images/ng.715-F1.jpg)
+
+###  6) Discussing
+------------
+- [:email:](https://github.com/BGI-shenzhen/PopLDdecay) [email protected] / [email protected]
+- join the<b><i> QQ Group : 125293663</b></i>
+
+
+######################swimming in the sky and flying in the sea ########################### ##