February 20, 2013

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.

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