README.txt 


(1) Sample commands for compiling the MCMC program:

   cc -o MCMCcoal -fast MCMCcoal.c tools.c -lm
   gcc -o MCMCcoal -O4 MCMCcoal.c tools.c -lm
   cc -o MCMCcoal -march=athlon -mcpu=athlon -O4 -funroll-loops -fomit-frame-pointer -finline-functions MCMCcoal.c tools.c -lm

   cl -O2 -Ot -Og -G6 -W3 MCMCcoal.c tools.c

(2) Sample commands for compiling the simulation program

Delete or Comment out (use /* and */ to braket the line) the following
line at the beginning of MCcoal.c.

#define MetropolisHastings

Then 

   cl -O2 -Ot -FeMCcoal.exe MCMCcoal.c tools.c
   cc -o MCcoal -fast MCMCcoal.c tools.c -lm
   gcc -o MCcoal -O4 MCMCcoal.c tools.c -lm
   cc -o MCcoal -march=athlon -mcpu=athlon -O4 -funroll-loops -fomit-frame-pointer -finline-functions MCMCcoal.c tools.c -lm


(3) ds for summarizing results.

The MCMCcoal program automatically summarizes results.  However, ds
(for descriptive statistics) can be used to read the data file
generated during the MCMC run and to summarize the results.  It
calculates the min, max, mean, SD, 95% CIs.  It also does
one-demensional and 2-dimensional kernel density smoothing.

To compile the program, use one of the following

   cl -O2 -Ot ds.c tools.c

   cc -o ds -O2 ds.c tools.c -lm

To run the program, 

   ds mcmc.out


Ziheng Yang
