Simply speaking, this tool is for scanning the Tajima D signals genome wide, incorporating the missing data and SNP calling/ reads mapping uncertainties. It also calculates many existing neutrality tests (without outgroup, currently). If you just type 

java –jar RobustScan.jar

the simple helping information will be prompted. 

The sample input file is as below:

22      14431249        TTTTTTTTttttttttTCttTTTTTTTTTTttcttttcTTttTTttTTttTTttTTttTTttTTTTttTTttttttctttCTctttttttttttttTTcttcTTtttttttttt   @~~~4~~~~~@~~~~~%5E4~Q~I~~M3~~M~1~~~U-QU~~~M~~~BM@~~U~@@~3~@C~~~~0~~~~@~~M~M-~~~1~1~~C~M~C~~3BM~~~/~~1~~~~UQG/~@~@

22      14432239        AGAGaaAAagaaagaaAAaaaaaaAAaaAAaaaaaaaaaaaaAAAAGAAAAAaaAAgaAAaaAAGAaaAAaaaaaaAGaaAGagaagaaaaaaaAAAAaagaGAggAAaaaaaa   R4~+O~~~~<R~~<~~ROQP~N~~T~~N~~~~O~M~dONc~~~~~~IR~Ri~c~RR+RPRd~~~JO~~~iRi~~M~O<~~O<O/id4~~d~iN~~~~~O~+OKM<+cNUU~R~R

22      14432250        AAAAAAAAaaaaaaaaAAaaaaaaAAAAAAaaaagaaaaaaaAAAAAAAAaaaaAAaaAAaaAAAAaaAAaaaagaAAaaAAaaaaaaaaaaaaAAAAaaaaAGaaAAaaaaaa   ~A~V~~~~~B~~~?~~~~)(~~~~+~~~~~~~~~$~~~~~?~~~~~-~~~=~~~~~V~'~~~~~(~~~~=~=~~$~~B~~~=~E=~C~~~~=~~~???~~V~$$?V~~~~~~~~
   
The first column is the chr number, the second is the location, the third is the genotypes of all individuals, the last is the corresponding qualities (the same encoding as fastq file).