Jalview old project

Hi everyone!

I am trying to open an old project (from 2004) published and available online in fasta format. Unfortunately, even by downloading the version 2.4 in Jalview archive, I did not succeed to open the project. I need to open the fast data in the old format and export the alignments to be compatible with Jalview 2.11.

Does anyone can help me with that?

Thank you!

Sorry to hear you are having trouble with this. Is the file a Jalview Project File or simply a .fasta file?

2004 pre-dates even Jalview 2.0 …

Can you share the reference to that file here so we can take a look?



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Thank you very much for answering. Sure I can share it!

Actually, I tried different versions and it was not possible to open the fasta data.

(Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome | BMC Genomics | Full Text)

Additional file 1: Lm SIDERs . Detailed representation of the data presented in The project can be opened and modified with the freely available JALVIEW software [8]. (ZIP 465 KB)

Thank you for your help @geoff.barton

Hi Gabriel,

I had a look at the file you linked to and it is an old format (the one linked to turns out to be from 2008, saved with Jalview version 2.3) but Jalview can still open it if you follow these steps:

  • Change the name of the file from 12864_2009_2124_MOESM1_ESM.zip to 12864_2009_2124_MOESM1_ESM.jar (i.e. just change the extension from .zip to .jar)
  • Launch Jalview (current release) and choose FileLoad Project
  • In the File Chooser window change the Files of Type to Jalview Project (old) (.jar)
  • Navigate to where you saved the file (as .jar) and you should see the file.
  • Select the file and click on Open as usual.

This should open both the FASTA data and a Newick tree saved within the old project file.
If you want to export just the FASTA data, go to the alignment window and choose FileSave As…; then change Files of Type to Fasta (.fa, …) and give it a filename with extension .fasta . You can also save the tree separately as a Newick file.

Alternatively, for future use in Jalview you can use the Jalview window FileSave Project as… and make sure the Files of Type is showing Jalview Project (.jvp)

Hope this helps! If not let us know and I can send you a .jvp version of the project file which should just work.

Best wishes,


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Hi Gabriel,
Hopefully Ben’s answer will help you? We changed the file extension for Jalview projects a while back, but they still should open in the current Jalview if you do as he suggests. Please let us know how you get on :slight_smile:

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Thank you very much @ben_soares! It worked finely!

my very best



Thank you @geoff.barton!

Ben solved the problem.



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No problem – any more issues you know where we are! :wink: