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
- Some scripts (including g3-iterated.csh) use the program elph, which
needs to be separately downloaded and installed. You can get it from
- Help on options and command parameters for each program can be gotten
by running the program with a -h option.