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5.5 Possible installation problems:

The following programs are required for correct execution of the makefile:

If any of these programs is missing, the program may not compile. The compiler options are based on the Gnu c++ compiler (g++ version 4.4.3). To compile with other compilers, set the CFLAGS variable with the appropriate flags for your compiler, i.e.

make CFLAGS=...

The use of awk and tee is for editing the configvars.h header file. If these programs are not available on your system, you can manually edit the configvars.template file to get your configvars.h, then run make with the setting NOAWK=1. (The value 1 is arbitrary, any value will do.) None of the other programs should present a problem. If there is a problem, you can manually compile the main executable cold by just compiling the following c++ files:

Main.cpp CommandLine.cpp Likelihood.cpp Matrix.cpp Miscellaneous.cpp Optimisation.cpp Parameters.cpp Sequence.cpp SignalHandler.cpp Tree.cpp TreeLikelihood.cpp Input.cpp Debug.cpp ErrorHandler.cpp MixTreeLikelihood.cpp

You will need to compile with support for pthreads. [I might try to create a version which can be compiled without this support if there are many problems with this.] Other compilation options are not essential, but using optimisation is recommended, and adding debugging information improves your chance of getting useful replies to any problems.