[Jalview-discuss] distance initialized to zero in average seq id tree?

[Daron Standley]

Dear Jalview experts,

I recently tried to draw a tree from an MSA in which some of the  
sequences were completely unaligned (e.g. a sequence fragment that  
aligned only to the N-terminal region and one that aligned only to  
the C-terminal region).  Oddly, these two sequences were placed  
together on the (average distance % id) tree, even though their  
distance would be undefined. This suggests that there is a bug in the  
Jalview tree code that (perhaps) initializes the distance to zero.  
Attached is the MSA that cases the problem. Two of the sequences that  
should not be close together are 1w0tA and MOUSEAkirin2.

Best regards,

Daron



Daron M. Standley, Ph.D.
Systems Immunology Laboratory
Immunology Frontier Research Center
Osaka University
Tel:   +81-(0)6-6879-4311
FAX: +81-(0)6-6879-8636




-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20081215/91ee0fbe/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: mafftash1.fa
Type: application/octet-stream
Size: 3589 bytes
Desc: not available
Url : http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20081215/91ee0fbe/attachment.obj 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/attachments/20081215/91ee0fbe/attachment-0001.html