SNPEM: E-M Algorithm Estimations of SNP Haplotypes

Use the form below to upload your data.  Data files uploaded are expected to be in SPACE separated lists of values having the format exemplified below:

Where:

• The first two rows contain the locus identifier and BAC identifier for each marker (simply repeat the locus identifier in the BAC row if BAC ID's are irrelevant to your experiment.)
• For the remaining rows, the first column is the sample identifier, the second column is the group identifier, and the remaining columns are the marker pair of each locus for the sample.
• The loci are expected to be listed in pairs for a given row in the file, as has been indicated above by alternating the foreground color between locus pairs of alleles.
• You can include comments in the file: if you place a hash ("#") at the beginning of a line the entire line will be deleted from the data before being passed on to SNPEM.

The program as it is currently written does not tolerate missing data, and can process a maximum of ten loci. An example data file you can use for input can be found here. A file is also provided to help you understand SNPEM's output, and it's input requirements.

If you wish to run SNPEM on your own computer, a windows executable file and source code are available in this zip file.