I am not sure. if there are any .o files, you can delete them first. also look at the dates and file permissions, in case they are wrong:
ls -lF
there is a file README.txt in the src/ folder. you can copy the commands onto the command line, and see whether the programs compile:
gcc -O3 -o baseml baseml.c tools.c
gcc -O3 -o basemlg basemlg.c tools.c
gcc -O3 -o codeml codeml.c tools.c
gcc -O3 -o pamp pamp.c tools.c
gcc -O3 -o mcmctree mcmctree.c tools.c
gcc -O3 -o evolver evolver.c tools.c
gcc -O3 -o yn00 yn00.c tools.c
gcc -O3 -o chi2 chi2.c
ziheng