Please download the latest version of Frealign from http://grigoriefflab.janelia.org/frealign and unpack the archive using
tar -xvzf archive.tar.gz
This should generate a new directory called frealign_v9.XX ("XX" will depend on the version of Frealign). Change the current directory to the directory (cd frealign_v9.XX) and type
This should display a line of text that must be included in the login shell script (bash or csh). Alternatively, include the bin subdirectory in your PATH variable. After including the line, either log out and back in, or type
depending on what type of shell is used.
You may also have to recompile the binary executables. The distributed binaries are compiled for Linux operating system. Makefiles are included for OSX.