GreenPhyl Information



12/07/2012

Release Notes of version 3

We are pleased to announce the release of a new version of GreenPhyl.

Database content
For this version some genomes were updated  and 6 genomes were added:
  1. Musa acuminata
  2. Theobroma cacao
  3. Manihot esculenta
  4. Phoenix dactylifera
  5. Cucumis sativus
  6. Malus Domestica
The source and the version of the sequences are listed in the documentation section.

Gene family Annotation
Since the version 2, more than 1500 additional clusters were annotated.

Website
The website was overhauled and redesigned using advanced Ajax and CSS technologies to offer better user-friendliness.

New tools
  • Quick search: A new way to explore the database based on identifiers or keywords.
  • IPR combination tool:  It allows to create you own clustering of sequenced based on combinations of Interpro domains.
Phylogenetic-based Pipeline
Our pipeline  has been modified. The masking of the multiple alignments is now performed by Trimal and the gene tree reconcilation is ensured by RAP-Green. The bootstrap procedure was replaced by the aLRT provided by PhyML. More details are available in the documentation.
Approximately 7000 gene families were analysed.

Please note that the version 2 will remain accessible. The version 3 is also accessible at the following address:
http://www.greenphyl.org/v3/

UPDATE (26/02/2016): old versions have been removed
Should you have any questions, please do not hesitate to contact us