I do not have those programs installed also. The very good solution is to run without them:
^make_fragments.pl -nosam -nojufo -noprof -verbose prefix_.fasta^
which requires only easy to get psipred.
Then get SS predictions from any server or metaserver (I use of course GeneSilico MetaServer which gives SS preds from many different programs as well as simple consensus prediction).
Edit 4-letter prefix_.psipred if You think that this secondary structure prediction is not correct,, carefully change the predicted secondary structure states as well as a confidence levels based on the external server results.
You have to generate fragments again: First delete files looking like this:
aaXXXX_03_05.200_v1_3 (3 aa fragments)
aaXXXX_09_05.200_v1_3 (9 aa fragments)
XXXX_.psipred_ss2 (ss in different format)
^pNNMAKE.gnu aa 4-letter prefix _^
This is potentially very good approach as you have total control on your starting SS preds, you can use many more external SS servers, and you do not need to install them locally.
> The same problem. Can’t find where to download jufo and sam programs.