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.jar (i.e. just change the extension from .zip to .jar)
- Launch Jalview (current release) and choose File → Load 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 File → Save 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 File → Save 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.