Hi Nicholas,
For running phastCons on the multiple alignments, we actually used two sets of
branch lengths: one for sequences expected to be conserved, and one for
sequences not expected to be conserved. See the last line ("TREE: ((...") in
these files:
http://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ave.cons.mod
http://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ave.noncons.mod
The branch lengths are shorter in ave.cons.mod -- depending on your purpose, if
you have to choose one then you'll probably want noncons.mod.
Hope that helps, and please email us at [email protected] if you have more
questions,
Angie
----- "Nicholas Price" <[email protected]> wrote:
> From: "Nicholas Price" <[email protected]>
> To: [email protected]
> Sent: Thursday, September 10, 2009 9:14:26 AM GMT -08:00 US/Canada Pacific
> Subject: [Genome] Drosophila spp. tree with branch lengths Newick format
>
> Hi
>
> I need a Drosophila species tree with the branch lengths, in Newick
> format....Is that available at genome.ucsc.edu...If yes, can you copy
> paste
> the link to the data file
>
> Thank you
>
>
> Nicholas
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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