tag:treefam.tenderapp.com,2013-02-16:/discussions/questions/8-manual-curation-in-treefam-9TreeFam: Discussion 2013-06-26T08:22:31Ztag:treefam.tenderapp.com,2013-02-16:Comment/274962002013-06-26T08:22:30Z2013-06-26T08:22:30ZManual curation in TreeFam 9<div><p>Dear Michael,<br>
thanks for your message.<br>
You are right, the TreeFam database was built - similar to Pfam and
Rfam -<br>
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)<br>
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.</p>
<p>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.<br>
That was reason enough to not curate families anymore.<br>
Bear in mind that there are three problems with the manual curation
of families:<br>
1. It is very time-consuming<br>
2. depends on subjective choices made by the curator (difficult to
come up with clear set of rules)<br>
3. the gene tree topology can change dramatically depending on the
input alignment.</p>
<p>I hope that helps. If not, please don't hesitate to ask for more
details.</p>
<p>Cheers,<br>
Fabian</p></div>Fabian