TOPALi requires the use of four external C++ applications, called Bambe, Barce, Fitch, and TreeDist.
These programs are pre-compiled and distributed with TOPALi for Windows and Mac OS X users, but for other systems they must be compiled separately (using the included makefiles).
By default, the source code for these applications will be installed into:
To install, simply change to the /binaries/unix folder and type sh compileprogs.
TOPALi will set up links to these files by default, but if you move the executables to another directory, TOPALi must be informed of their location by selecting Analysis | Analysis Settings from TOPALi's main menu bar.