Hi Brooke, Thanks for your reply.
Actually I was wondering whether you have performed evofold based on the alignment of 14 species in your multiple alignment download (http://hgdownload.cse.ucsc.edu/goldenPath/dm3/multiz15way/ ) or just the Drosophila species (without A. gambiae, A. mellifera and T. castaneum)? And in this case what is the phelogenetic tree used? Thanks and Regards, Richard On Mon, 2008-11-10 at 13:34 -0800, Brooke Rhead wrote: > Hello Richard, > > The EvoFold track uses the information in the "Conservation" and "Most > Conserved" tracks (in the Comparative Genomics track group). > > Note that the EvoFold track on dm3 (D. melanogaster, Apr. 2006) consists > of items converted via liftOver from the dm2 assembly (D. melanogaster, > Apr. 2004). Therefore, both dm2 and dm3 Evofold tracks use the dm3 > "Conservation" and "Most Conserved" tracks. > > You can get to detailed information on both tracks by clicking on the > blue track name on the main Genome Browser page > (http://genome.ucsc.edu/cgi-bin/hgTracks). The Conservation track > details include a list of assemblies that were used for the Multiz > alignment, as well as the phylogenetic tree used to generate the > multiple alignment. > > I hope this answers your question. Please feel free to write back to > [email protected] if you have further questions. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 11/09/08 17:42, Richard Lin Zhou wrote: > > Is it possible to provide the parameters that were used to generate the > > EvoFold track in the Tables on D. melanogaster? (The Phelogenetic tree > > and alignment input etc). > > > > _______________________________________________ > > Genome maillist - [email protected] > > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
