Hi all,   Thank you very much for the overwhelming response to my query about a program that can identify, count and group together same haplotypes. Below I paste the suggestions with the names of people who sent them (please excuse me anybody who could have been left out). Thanks again,   Luis   Fabox softwares: http://www.birc.au.dk/fabox/   Sandrine Sebastien Palle Villesen Fredsted   DAMBE (http://dambe.bio.uottawa.ca/dambe.asp) or collapse (http://darwin.uvigo.es/software/collapse.html) Paulo Anna Francesco Nardi Yael Kisel Diana Catarino Natalia Martinkova Maarten Vonhof Joel Anderson John Switzer   TCS will do this. http://biology.byu.edu/Faculty/kac/crandall_lab/docsdata/pdf_files/2000/TCS-ME1.pdf Amber David Posada Judith Fehrer Romina Piccinali     DNAsp (http://www.ub.edu/dnasp/).   Cornelya Kluetsch Sibelle Torres Vilaça     Bioedit could probably also be made to fit the bill quite easily (Edit>Search>Find Non-unique sequences and concatenate titles)depending on the scale of the problem Darren Obbard   DOTUR, http://schloss.micro.umass.edu/software/dotur.html, can group sequences into operational taxonomic units defined by different percentage similarities Richard   Holly Mortensen also suggested using Arlquin, but that is the program I have been using and I could not find an option for it to group same haplotypes together (it may be that I am not very good at searching, as you can tell by my original question). Luis Marquez