Im trying to detect positive selection in promoter regions using Fedrigo method. They have written a batch file code for HyPHy GUI (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) , I have a few problems in there:

1)      Both links for downloading HyPHY in source code for building command line version of hyphy seems to be broken! I checked this page a few times(Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) ,is there specific instructions for downloading it or im in the wrong page or for downloading from Japan i need to download from a different server?
2)      Fedrigo’s method is written for hyphy GUI. if command line version of hyphy is possible, how can I give inputs(neutral proxy alignment,promoter alignment,tree…) to the command line code, is it in regular command line input argument format  as “–input path”  like T_COFFEE or NCBI BLAST packages or like the way PAML package works by getting a single .ctl file for all the input addresses and parameter values?
I know these might seem strange questions but I'm a biologist and not so expert in computer science

Thanks,
Masyh