PRGmatic reformats next-generation sequencing into diploid loci. It is described fully in Hird, Brumfield and Carstens (2011). PRGmatic reformats next-generation sequencing into diploid loci. It is described fully in Hird, Brumfield and Carstens (2011). 
lociNGS displays large multi-locus datasets and reformats data. I worked on this project for Google Summer of Code 2011 with NESCent.