I am trying to download pairwise ortholog/paralog predictions from TreeFam-A (thus data from curated trees). However on the TreeFam download page I can't find how to download this dataset or how to distinguish TreeFam-A homologs from TreeFam-B homologs in the pairwise files. Is there a method of doing this or has TreeFam-A been discontinued?
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Support Staff 1 Posted by Matthieu Muffat... on 02 Jun, 2016 11:35 AM
The distinction between TreeFam-A and TreeFam-B does not apply to the
last release of TreeFam
2 Posted by Bas Verbruggen on 02 Jun, 2016 11:44 AM
Thank you Matthieu,
I assume the latest release is more akin to TreeFam-B and no longer contains manually curated data?
In a recent paper (see below) regarding orthologs it was stated that a Treefam-A dataset was used. They specifically state Treefam-A version 7 and refer to this website (http://www.treefam.org/).
Are older version of TreeFam still available for download? (specifically the version mentioned above)
Altenhoff et al. Standardized benchmarking in the quest for orthologs Nature Methods 13, 425–430 (2016)
Support Staff 3 Posted by Matthieu Muffat... on 02 Jun, 2016 01:40 PM
This is correct: all the families should be considered as TreeFam-B
In this paper's analysis, they downloaded the data from the previous
databases, which are still available. The website, on the other hand,
only shows the latest data
The database is on a MySQL server available at
mysql-treefam-public.ebi.ac.uk on port 4418 with the user "treefam_ro"
and no password
4 Posted by Bas Verbruggen on 02 Jun, 2016 01:51 PM
Thank you very much for your help Matthieu. I'll try to fetch the data from the MySQL server.
Matthieu Muffato closed this discussion on 02 Oct, 2017 01:25 PM.