Updated !

Details of the update are as follows:

New Ensembl release 70 and EnsemblGenomes Metazoa release 17

Data sets derived from 'Ensembl' and 'EnsemblGenomes Metazoa' have been updated to adhere the latest releases.


New species

Pacific oyster (Crassostrea gigas)

wasp (Nasonia vitripennis)

Southern platyfish (Xiphophorus maculatus) according to Ensembl release 69 and later

Ferret (Mustela putorius furo) according to Ensembl release 69 and later


Altered partitioning between Database 5 & 6

Previously, sequences of the sea lamprey (Petromyzon marinus) were included in Database 5 together with other vertebrates available at Ensembl, while Database 6 has only a single cartilaginous fish, Callorhinchus milii. In the latest setting, sea lamprey sequences are included in Database 6, labelled 'Non-osteichthyan vertebrates'.


'Category ID'

Previously, only sequences from genome-wide resources (also human RefSeq data set) had Species ID (e.g., 'HOMSA' for human) which is recognized at  data set refinement steps the MAFFT server.

To give visual cues for sequences derived from NCBI Protein (Database 7 and 13), I have introduced 'Category ID', which is explained in the table in the 'Species' page .


Additional notes

In parallel with the improvement of the aLeaves server, the interactivity of the MAFFT server is also being improved, in order to better process data sets forwarded from the aLeaves server. Please also try the improved work flow between the two servers by clicking on the link under 'Proceed to tree building' in aLeaves results page.

Database update scheduled today

The databases available at aLeaves will be replaced today to cover more species and sequences, I am sorry if you have some inconvenience because of this.

I will announce again when done.

An update of databases scheduled in mid Feb

I plan to update some aLeaves databases in mid February. The change will include the adoption of the latest Ensembl release.

Digest of updates in the first phase

December 25, 2012 - Two lophotrochozoans (Capitella teleta and Helobdella robusta) were added to the Database #11, following publication of the study involving resources of these genomes (Simakov et al., 2013. Nature).

December 11, 2012 - New function to pass the output to a clustering tool (powered by the MAFFT server) added (still tentative version).

December 7-8, 2012 - Server shutdown because of annual scheduled energy shutdown of RIKEN CDB. 

December 4, 2012 -  Release of non-restricted version.

November 19, 2012 -  Release of beta version (restricted with password).

Beginning this blog site

This blog site has been initiated to announce changes in the aLeaves web server.