Full instructions for installing and running Glimmer are in file glim302notes.pdf in this directory. Here's a quick start guide for the inpatient: - To build all Glimmer programs, go to the src directory and type make (or alternately gmake). This will create all the executable files in the directory bin. Note that initially directories bin, lib and obj are all empty. - Scripts for running the programs are in directory scripts. Each needs to be edited near the top to specify the correct location (give the full path) where you have the bin and scripts directories on your system. Script g3-iterated.csh is generally the best to use to make gene predictions from a single genome sequence without other data. - Some scripts (including g3-iterated.csh) use the program elph, which needs to be separately downloaded and installed. You can get it from ccb.jhu.edu/software/ELPH/index.shtml - Help on options and command parameters for each program can be gotten by running the program with a -h option.