branch length calculation

[Hoa Nguyen]

Hello,

I extracted my list of species from 120way.nh file:

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/hg/utils/phyloTrees

What are the tree's branch lengths based on?

Do you have any documentation links or references about the tree's lengths?
Thanks,
Hoa

[Brian Lee]

Dear Hoa,

Thank you for using the UCSC Genome Browser and your question about the conservation track's phylogenetic tree.

If you navigate to the Track Description page, you will find much useful information to review about the track and related data: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons100way

Reading through the documentation you will find details in the Methods section under "Phylogenetic Tree Model" and the following line in the "Credits" section, followed by the following reference listed at the bottom under the "References" and "Phylogenetic Tree" section.

The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community. Thanks to Giacomo Bernardi for help with the fish relationships.

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply togen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

--

[Hiram Clawson]

The actual branch lengths are calculated at UCSC from a 4d sites calculation
with the phyloFit program. Please note the procedures at the section starting:

# Phylogenetic tree from 100-way (DONE - 2013-09-13 - Hiram)

In the hg19.txt file:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/hg/makeDb/doc/hg19.txt

This is mentioned on the details page:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons100way

at the section: "Phylogenetic Tree Model"

--Hiram