[Gmod-help] Re: Phylogenetic display in Gbrowse

[Nick Erndt]

Thanks so much for the response Mark,

I'll look into this in early January.

We currently have a Haplotype Viewer that can show haplotype similarities between mouse strains, but a cladeogram or dendogram would be a much more effective display.

Here's a link to our Haploytpe Viewer:

http://mouse.perlegen.com/mousehap37/blockview.cgi?s1=9&s2=10&s3=12&s4=13&s5=0&s6=1&s7=2&s8=3&s9=4&s10=5&s11=6&s12=7&s13=8&s14=11&s15=14&s16=15&chr=0&from=0&to=0&qpos=Chr06%3A115897546..115904449


Take care,
Nick

 
Nick Erndt
nerndt at yahoo.com
hm 650 493-7607 mobile 650 906-5970



----- Original Message ----
From: Mark Ok <mokada23 at hotmail.com>
To: nerndt at yahoo.com; gmod-gbrowse at lists.sourceforge.net; help at gmod.org
Sent: Monday, December 24, 2007 1:45:43 PM
Subject: Phylogenetic display in Gbrowse

Hi all,

My name is Mark and I am the student that worked on a Phylogenetic track during the summer with Lincoln Stein.  I will summarise what I have implemented and plan to do in the next while.

The idea of the track is to display an alignment of multiple species alongside a simple cladogram.  When zoomed in, a DNA alignment is drawn and when zoomed out, a log-scale histogram of the alignment scores are drawn across the species.
+-------------------------- the track ----------------------+
|+====================== the cladeogram glyph==============+|
||                                                         ||
||+--------------alignment glyph 1------------+ ---|       ||
||                                                 |--|---cladeogram
||+--------------alignment glyph 2------------+ ---|  |    ||
||+--------------alignment glyph 3------------+ ------+    ||
| +=========================================================+|
+-------------------------- the track ----------------------+

The track makes use of:
-Gap details from the GFF3 format attribute (as explained in http://www.sequenceontology.org/gff3.shtml).
-Cladogram data from a tree file readable with Bio::TreeIO

A simple example is explained in an edited version of the tutorial at:
gbrowse/tutorial/tutorial.phyTreeEdit.html
of the head version.

Right now I am in attempting to incorporate Lincoln's libraries which will allow Wiggle and Dense files to be drawn for the alignment scores.

This track is still a work in progress and I apologise for my slow pace since the summer.  I am also a beginner at programming gbrowse as well as in phylogenetics in general and would appreciate any feedback.

thank you very much,
Hisanaga Mark Okada




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