Manual curation in TreeFam 9
In the old days, there was the distinction between TreeFam-A and TreeFam-B (manually curated vs. automatically generated). I don't see this anymore on the TreeFam 9 website or in the download files. Did I just not find it? Or are there no manual checks anymore?
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1 Posted by Fabian on 26 Jun, 2013 08:22 AM
thanks for your message.
You are right, the TreeFam database was built - similar to Pfam and Rfam -
with the idea of having an A- and a B-section. (You are also right that there is currently no documentation about this, which we will add shortly)
Up to release 4 or 5, TreeFam put a lot of effort into manually curating TreeFam A families, or curating TreeFam-B families that would then move into TreeFam-B.
As you might know, TreeFam uses TreeBest to build reconciled gene trees for every family. At some point it was tested whether the trees build from TreeBest are as good as the ones that were manually curated. Turned out, they are equally good.
That was reason enough to not curate families anymore.
Bear in mind that there are three problems with the manual curation of families:
1. It is very time-consuming
2. depends on subjective choices made by the curator (difficult to come up with clear set of rules)
3. the gene tree topology can change dramatically depending on the input alignment.
I hope that helps. If not, please don't hesitate to ask for more details.
Fabian closed this discussion on 26 Jun, 2013 08:22 AM.