Jalview Project Archives
These are java archives of an XML file containing alignments, trees and Jalview display information. A data exchange standard is currently being developed, so there is no stable schema yet, but Jalview web services will soon make use of the same interchange format.
For those who want to know...
Jalview uses java classes automatically created using Castor. Jalview 2.08 uses descriptor classes which significantly increase the speed of marshalling / unmarshalling java objects into XML. Files created prior to Jalview 2.08 can still be read in, but they will be saved in the new format.