ATLAS (link1, link2) is a Java based tool to manage genotypes. It is handy, but notoriouslly frustrating to install, since there are several different instructions about how to install it - I am not talking about different instructions at different places (say on the net), but in the distribution package. This is very very confusing. I have just spent more than half an hour to install it and I remember I had the same problem last time I tried to install it. The correct instructions are in the ATLAS.html file and this should be done:
  1. Create ATLAS directory in your user home directory, say "C:\Documents and Settings\GGorjan"
  2. Add the following files to this folder (Atlas.jar, atlas.ini, chr.atl, ATLASman_v1.4.pdf, ATLAS.html)
  3. Create directory ATLAS_files such as "C:\Documents and Settings\GGorjan\ATLAS\ATLAS_files" and put all figures and html files in there

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