PFAM alignment retrieval not working in

The Pfam web service is in the process of moving to a new server run by InterPro.
The old Pfam server was decommissioned on 5th October and so Jalview’s Sequence Fetcher for PFAM (Seed) and PFAM (Full) has stopped working.

We have a patch release already available via Jalview Test but if you need to retrieve alignments from Pfam in Jalview right now, we have a couple of workarounds:

  • Edit your ~/.jalview_properties file (that is, the file called .jalview_properties found in your user home folder/directory) to add the line:

or alternatively you could use the InterPro site to download a gzipped Stockholm file:

    1. Open the InterPro Pfam Alignment page for your accession ID in a browser at (replace PF10002 with your accession ID.
    2. In the Available alignments drop-down list that appears choose seed or full (or something else).
    3. Click on the turquoise Download button on the right to download a gzipped Stockholm file.
    4. This file can be opened directly in Jalview in any usual way – the easiest being just to drag and drop it onto an already running Jalview Desktop.

If you have any problems with either of these methods, please send a message in the discussion category to let us know.

(if you use the first method, when Jalview updates to use the new InterPro server it will automatically remove this pfam-legacy setting for you so that the Pfam sequence fetcher continues to work when the legacy server is turned off in January 2023)