There are several packages, I assume you took the tar.gz compressed package. The documentation is in the compressed archive, extract it: a README file (). You need to have installed perl and a c-compiler as a precondition to build this, doing this on windows will be more complicated than on linux, if on windows you probably need cygwin for the compilation. Extract the archive like so:

tar xvzf estscan-[?].tar.gz

The README says:

This is a Perl module. It requires my BTLib module, which should be located in the parent directory of this one. They can be built and installed like any other Perl modules:

  cd <BTLib directory>
  perl Makefile.PL
  make install

Actually the BTLib directory is the one you just extracted. To install it globally you might add sudo. Then run ESTscan, it is a perl program. Good luck

The latest version ESTScan 3.0 is entirely written in C that bypasses some perl module problems, download and compile that.You can download it from HERE

It is actually easier to have EstScan3 to run. As pointed out by WoA, EstScan3 is written in C, but the output is identical.

There are eight steps to follow

1. Go to http://sourceforge.net/projects/estscan/files/
2. get the tar.gz of estscan version 3 (estscan)
3. get the tar.gz BTlib latest version (BTLib)
4. get your *smat file from the closest organism (matrices)
5. (optional) if you want to generate you own *smat, follow the manual (documentation)
6. Untar/gunzip everything

7. Install the BTlib perl libraries (thanks Michael)

   cd BTLib
   perl Makefile.PL
   make
   sudo make install
   

8. Compile Estscan

   cd Estscan
   gcc -o estscan estscan.c
   chmod 750 estscan
   

Now you should have a fully functional estscan. You just need to input the matrix file and the fastas.

Like:

./estscan -M matrix.smat yoursequences.fasta

Good luck!