TreeFam 9 is now available!

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)

Getting all Pfam-A domains for a proteome

We’ve had a few helpdesk tickets in the last few months asking how to download all of the Pfam-A domains for a particular species. This information can be quite difficult to obtain: getting it requires either downloading and installing a sub-set of the tables in our MySQL database, or else searching all of the sequences from the species of interest against Pfam, probably using our batch search.

We thought it would be useful to simplify the process and add the domain information directly to our proteome pages, so we’ve just done exactly that.

The Pfam website in a virtual machine

Since releasing the new Pfam website four years ago, we’ve had a steady trickle of mails from users who would like to install and run the site within their own local environment. It used to be possible to do just that, given a following wind, if you were ready to install the site from its source code. Unfortunately, after some internal changes and as the list of Perl module dependencies grew and grew, the process got harder and more complex and eventually we stopped supporting it entirely. We’ve been actively discouraging people from trying this for far too long, all the while promising to make the process easier. Finally we’ve managed to get around to building a virtual machine (VM) that should make the whole thing possible again.