[Gmod-help] Phylogenetic display in Gbrowse

[Mark Ok]

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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