There are many softwares wich can calculate Nei,s genetic ditance and to estimate confidence of binary data like 0,1. Try these softwares which are free ARlequin, Genalex, Pop Gene, Multilocus and many more. But you sholud be able to make input file. A software is there CONVERT which uses Excel as input file (Text Tab Delimited) and then convert the data in to many softwares. Good luck and try these
I'm using TFPGA. It is simple to use but provide many options. It is free. You can find it at http://www.marksgeneticsoftware.net/tfpga.htm. If not, I believe that I still have installation file.