There are two versions available - SGI and Linux. They can be downloaded from the following links:
Note: The binaries hmmbuild and hmmconvert are part of the HMMER2 package, they have been included in this binary distribution to make your life easier. However, please see http://hmmer.wustl.edu/ for the most recent version of HMMER2, and further information about HMMER2 in general.
James is no longer in the group so the amount of support we can give is pretty limited, but if you do have problems you can mail us at www-jpred@compbio.dundee.ac.uk and we'll try to help.
More platforms may be available later.
There is also some initial documentation with licence details available:
At the moment, the PSIBLAST perl parsers included in Jnet have only been tested with BLAST reports generated by version 2.0.3 of PSIBLAST. However, separate perl scripts are available here, that will parse the latest version of PSIBLAST (2.0.10) and generate the alignment profiles needed for Jnet. The scripts have not been fully tested. These parsers also have an added side effect of being able to extract the multiple sequence alignments in fasta format, so that you can view the multiple sequence alignments from PSIBLAST directly in programs such as Jalview (for details, see the README in the TAR file). Alternatively, an SGI binary version of blastpgp version 2.0.3 can be downloaded here (670Kb) which will work with the parsers included in the original Jnet distribution.
An alpha (0.1) version of the source is available, a C compiler is required:
Note: The Jnet method requires the hmmbuild and hmmconvert programs of the HMMER2 package, the source for these programs can be found here