Hi Jake, Our models for conserved and nonconserved sites' substitution rates are estimated from bases that we were able to align across species, so right there is a big source of bias towards bases that have not diverged beyond recognition. The "four-fold degenerate positions" subst/site must have been estimated by a different method from the trees that we feed into phastCons.
BTW If you would like to see the "makedoc", the file is kent/src/hg/makeDb/doc/dm2.txt in our source tree (http://hgdownload.cse.ucsc.edu/admin/jksrc.zip or see http://genome.ucsc.edu/admin/cvs.html if you use CVS), and has all the gory detail of how we generated the track. Search for the "PHASTCONS 15WAY" section. I hope that helps, and please let us know at [email protected] if you have more questions. That said, Adam Siepel (at Cornell now) created the estimation methodology behind our conservation scores, so if you really want to get into the finer points of the statistical basis for the estimates, he's the best source. Angie ----- "Jacob Biesinger" <[email protected]> wrote: > From: "Jacob Biesinger" <[email protected]> > To: [email protected] > Sent: Friday, December 11, 2009 5:39:52 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] Drosophila 15 way phylogeny? > > Hi! > > I've pulled up an old thread talking about the Drosophila 15-way multiz > phylogeny at > https://lists.soe.ucsc.edu/pipermail/genome/2007-January/012530.html > > I see the conserved and non-conserved posterior estimates, and the prior > estimate from the "makedoc:" > > >* This is from our makedoc for the 15way Conservation: > *>* > *>* #TREE: > *>* > (((((((((dm2:0.032478,(droSim1:0.017650,droSec1:0.015740):0.017736):0.026088,(droYak2:0.058116,droEre2:0.055952):0.031922):0.084953,droAna3:0.218988):0.051563,(dp4:0.013624,droPer1:0.015374):0.210705):0.046101,droWil1:0.292357):0.019351,((droVir3:0.109131,droMoj3:0.142623):0.047595,droGri2:0.154583):0.189999):0.113599,anoGam1:0.357817):0.092848,apiMel2:0.386309):0.169225,triCas2:0.169225); > *>* > * > > So this is the tree used as a prior. Although the overall topology is > similar to what I've seen before (i.e., > http://web.archive.org/web/20080413030437/http://rana.lbl.gov/~dan/trees.html) > I'm a bit confused because the total branch length for the tree is only ~ > 3.14. According to the original 12 drosophila sequencing paper, the branch > length estimated for four-fold degenerate positions was ~4.5 for the 12 > drosophilids alone. In this prior tree, the branch length for the > drosophilids are only ~1.85. Where exactly is this phylogeny coming > from? > > > Thanks! > -- > Jake Biesinger > Graduate Student > UC Irvine > (949) 231-7587 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
