Update & Best wishes for 2014 !

The aLeaves databases have been updated. As always, they includes the latest sequence sets at NCBI Protein for the covered taxa and the latest release by Ensembl and EnsemblMetazoa. This update newly includes 9 species below. Original data sources are linked from the species' names.


Database #3 (Non-human eutherians)

 Ovis aries (sheep)


Database #4 (Non-mammalian vertebrates)

  Chelonia mydas (green sea turtle)

  Chrysemys picta (painted turtle)


Database #5 (Actinopterygian fish)

  Astyanax mexicanum (Mexican cavefish)

  Lepisosteus oculatus (Spotted gar)


Database #6 (Cartilaginous fishes and cyclostomes)

  Lethenteron japonicum (or L. camtschaticum?; Japanese lamprey)


Database #9 (Arthropods)

  Dendroctonus ponderosae (mountain pine beetle)

  Solenopsis invicta (red fire ant)


Database #12 (Non-bilaterian metazoans)

  Mnemiopsis leidyi (comb jellyfish)


From now on, aLeaves runs 'blastp' of BLAST+ instead of 'blastall' of the 'legacy BLAST'.

Plus, this upgrade includes the change of the timing with which users are guided from the aLeaves server to the MAFFT server, after the search. In brief, the setting page for subsequent clustering process was previously still in the aLeaves server, but now is in the MAFFT server. Thus, users are warned about this in the first page of aLeaves execution.

aLeaves paper now available

An article introducing aLeaves and its link with the MAFFT server has been made available online just a few days ago.


This article will be a part of the Web Server Issue 2013 of Nucleic Acids Research.

Citation details:
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
Shigehiro Kuraku, Christian M. Zmasek, Osamu Nishimura and Kazutaka Katoh
Nucleic Acids Research. Web Server Issue 2013, in press.