On Unix, unzip the file using: tar -zxvf SeqSIMLA2.tar.gz. On Windows, unzip the file using programs such as Winzip or 7-ZIP.

There will be several directories in the folder.
bin: there are pre-compiled executable files for UNIX and Windows.
example: some examples and commands for running SeqSIMLA.
src: SeqSIMLA source code.
convert: source code for the tool to generate a reference sequence file.

You can also compile the source code. The C++ library Eigen needs to be downloaded from Extract the Eigen library to a folder. In the makefile, please change the path to the eigen library. For example, if you placed the eigen library in /home/test_user/Eigen, specify -I /home/test_user/Eigen in FLAGS in makefile. Then on UNIX, type
to compile the source code. An executable binary file SeqSIMLA will be generated.