You'll need to have GSL (Gnu Scientific Library) installed on your system, version 1.11 or later. Version 1.10 is the first GSL version that contains the required hypergeometric functionality. However, it has a bug that may cause negative probabilities to be computed (as a result of computing the wrong tail). This bug was fixed for 1.11 (as of writing the latest version). In the Makefile, the variable GSLPREFIX needs to be set to the proper value. It should be such that $(GSLPREFIX)/lib contains the GSL libraries (libgsl.a libgslcblas.a and/or the .so variants of these). $(GSLPREFIX)/include contains the GSL header files -- these will be in the directory $(GSLPREFIX)/include/gsl If, for some reason, on your system the GSL library files and header files do not share the same prefix as described above, make the necessary modifications in the Makefile -- it should be straightforward. After you have done this, typing 'make fast' should create a functioning sylamer executable. sylamer --help or sylamer -h gives a synopsis of available options. The manual page is available in in the /doc directory in HTML (sylamer.html), PDF (sylamer.pdf), PostScript (sylamer.ps), text format (sylamer.txt) and as a UNIX manual page (troff format, sylamer.1). The R script run_sylamer_and_plot_result.R (in the directory R_scripts) can be used to create word significance landscape plots using Sylamer. It accepts a number of parameters, which can be changed by editing the script. The script can be used as a starting point for further customization and automation. To do an example run, go to the R_scripts directory, and issue R --vanilla < run_sylamer_and_plot_result.R If you have questions or comments about this program please send a message to svd at sanger dot ac dot uk .