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<DIV>Thanks so much for the response Mark,</DIV>
<DIV> </DIV>
<DIV>I'll look into this in early January.</DIV>
<DIV> </DIV>
<DIV>We currently have a Haplotype Viewer that can show haplotype similarities between mouse strains, but a <FONT face="Courier New">cladeogram or dendogram would be a much more effective display.</FONT></DIV>
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<P><FONT face="Courier New">Here's a link to our Haploytpe Viewer:</FONT></P>
<P><FONT face="Courier New"></FONT> </P>
<P><FONT face="Courier New"><A href="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">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</A></FONT></P>
<P><FONT face="Courier New"></FONT> </P>
<P><FONT face="Courier New"></FONT> </P>
<P><FONT face="Courier New">Take care,</FONT></P>
<P><FONT face="Courier New">Nick</FONT></P>
<DIV><BR> </DIV>Nick Erndt<BR>nerndt@yahoo.com<BR>hm 650 493-7607 mobile 650 906-5970
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: Mark Ok <mokada23@hotmail.com><BR>To: nerndt@yahoo.com; gmod-gbrowse@lists.sourceforge.net; help@gmod.org<BR>Sent: Monday, December 24, 2007 1:45:43 PM<BR>Subject: Phylogenetic display in Gbrowse<BR><BR>
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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 <A href="http://www.sequenceontology.org/gff3.shtml" target=_blank>http://www.sequenceontology.org/gff3.shtml</A>).<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>
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