I’m working on an update to Metaxa that will bring at least double speed to the program (and even more when run on really large data sets on many cores). While there is still no real release version of this update (version 1.1), I have today posted a public “beta”, which you can use for testing purposes. Do not use this version for anything important (e.g. research) as it contains at least one known bug (and maybe even more I haven’t discovered yet). I would appreciate, if you are interested, that you download this version and e-mailed any bugs or inconsistencies found to me (firstname.lastname[at]microbiology.se).
Note that to install this version, you first need to download and install the current version of Metaxa (1.0.2). Then the new version can be used with the old’s databases.