I used a 20-component Dirichlet mixture prior that is provided by UCSC, here is the website:
The prior as defult in this program is called "recode4.20comp". But the order of the amino acid letter is different, they use "ACDEFGHIKLMNPQRSTVWY", but I use "ARNDCQEGHILKMFPSTWYV". Make sure the prior and the order of letters are consistent.
Thanks for your interest of using the codes. First, upload the folder to your server if you have not done so. Then enter the sub-folder codes. And the .c file you mentioned is find_patternwindow_v4_1.c
that's a computing function written in c language. Other than directly using the usual gcc compiler, you need to use mex to compile it so that the function can be called by your matlab scripts.
type "mex -setup", then you may be given several options. In linux/unix I recommanded, you just chose the first option that use gcc-mex compiler. When you are asked whether to overwrite the file mexopts.sh, you answer is yes. Then the next is simply to type
you will find that an executable file
is created. Then you have matlab function
find_patternwindow_v4_1() to use.