[Genome] Branch lengths of the Newick tree for 12 insect genome alignments

[Robert Kuhn]

Hello, Shu-Ning,

Here is the answer to a similar question from our mailing--list
archives (searchable at http://genome.cse.ucsc.edu/contacts.html): 

 http://www.soe.ucsc.edu/pipermail/genome/2007-January/012530.html

Note that the same tree was used in the dm3 conservation track.

Please contact the list again if this does not sufficiently answer
your question.

best wishes,

		--b0b kuhn
		ucsc genome bioinformatics group




> From genome at soe.ucsc.edu  Thu Dec 13 08:00:55 2007
> To: genome at soe.ucsc.edu
> Subject: [Genome] Branch lengths of the Newick tree for 12 insect genome
> 	alignments
> 
> Hi! I have gotten the topology of 12 insect species used in UCSC 12 flies,
> mosquito, honeybee, beetle multiz alignments by following the steps below:
> 1) pick a genome region of interest
> http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr2L:17649866-17739521&hgsid=100794076&flyBaseGene=pack&hgFind.matches=CG7100%2DRL
> ,
> 2) click on conservation of sequences
> http://genome.ucsc.edu/cgi-bin/hgc?hgsid=100794076&o=17649865&t=17739521&g=multiz15way&i=multiz15way&c=chr2L&l=17649865&r=17739521&db=dm3&pix=620
> 
> 3) scroll down to the methods at the bottom of the page
> 
> (((((((((dm3 (droSim1 droSec1))
>        (droYak2 droEre2)) droAna3)
>      (dp4 droPer1)) droWil1)
>    ((droVir3 droMoj3) droGri2))
>   anoGam1) apiMel3) triCas2)
> 
>       However, as for branch lengths, I couldn't find it either on the
> website or in the references. Could you help me with it or point me to the
> references? Thanks a lot!
> 
>       Bests,
>            Shu-Ning
> 
> 
> -- 
> Shu-Ning Hsu, PhD,
> Postdoctoral fellow,
> Dept. Microbiology and Molecular Genetics,
> University of California at Irvine
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