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
