TreeFam 9 is now available!

May 3, 2013

We are happy to announce that TreeFam 9 is online and you can find it under http://www.treefam.org.

TreeFam 9 now has 109 species (vs. 79 in TreeFam 8) and is based on data from Ensembl v69, Ensembl Genomes v16, Wormbase and JGI.

This release marks an important step for TreeFam as it is the first release build since TreeFam has been resurrected.
Here is a list of the most important changes in TreeFam 9:

  • New website layout (adopting the Pfam/Rfam/Dfam layout)
  • Infrastructure move of web servers and databases to the EBI
  • Sequence search against the library of TreeFam family profiles
  • new tree visualisations in pure javascript using D3, e.g. see the BRCA2 gene tree here.
  • Pairwise homology download

We hope you find all the information you are looking for. If you don’t, please let us know so that we can include the information you want. The old website will remain online here.

If you have questions, suggestions or find bugs, don’t hesitate to contact us through our new forum here.

Happy treefamming,

the TreeFam team
(Fabian, Mateus)

2 Responses to “TreeFam 9 is now available!”

  1. Albert Ries Says:

    Dear TreeFam admins,
    I cannot access the TreeFam mysql server by script. I get
    ‘Unknown MySQL server host ‘mysql-treefam-public”.

    IHO the ‘-host’ string in registry/production_treefam_reg_config.pl
    (line 56) is wrong:
    # Master
    Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(
    -host => ‘mysql-treefam-public’,
    -user => ‘treefam_ro’,
    -pass => ”,
    -port => 4418,
    -species => ‘TreeFam’,
    -dbname => ‘treefam_production_9_69′,
    #-dbname => ‘treefam_homology_67hmm’,
    );

    I would appreciate if you could provide the correct IP-address since I want to generate a couple of customized gene trees for a grant application.

    • fabsta Says:

      Dear Albert,
      thanks for your email and apologized for the wrong database connection parameters.

      It should be “mysql-treefam-public.ebi.ac.uk”. We fixed that on github.
      You can fix that line in the file: “registry/production_treefam_reg_config.pl”

      Let us know if we can help you with generating custom gene trees.

      Cheers,
      Fabian


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