<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'>
Hi all,<br><br>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.<br><br>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.<br><span style="font-family: Courier New,Courier,Monospace;">+-------------------------- the track ----------------------+</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">|+====================== the cladeogram glyph==============+|</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">|| ||</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">||+--------------alignment glyph 1------------+ ---| ||</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">|| |--|---cladeogram</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">||+--------------alignment glyph 2------------+ ---| | ||</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">||+--------------alignment glyph 3------------+ ------+ ||</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">| +=========================================================+|</span><br style="font-family: Courier New,Courier,Monospace;"><span style="font-family: Courier New,Courier,Monospace;">+-------------------------- the track ----------------------+</span><br><br>The track makes use of:<br>-Gap details from the GFF3 format attribute (as explained in http://www.sequenceontology.org/gff3.shtml).<br>-Cladogram data from a tree file readable with Bio::TreeIO<br><br>A simple example is explained in an edited version of the tutorial at:<br>gbrowse/tutorial/tutorial.phyTreeEdit.html<br>of the head version.<br><br>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.<br><br>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.<br><br>thank you very much,<br>Hisanaga Mark Okada<br><br><br /><hr />Your chance to win great prizes with TELUS and Windows Live Messenger for Mobile. <a href='http://www.telusmobility.com/on/wweb/instant_messaging.shtml' target='_new'>Click here for more information!</a></body>
</html>