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

[James Procter]

Daron Standley wrote:
> 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.  
ah. yes. it does look like something strange is going on there - this is
a good test case. I verified jalview's UPGMA implementation some time
ago, and it looks like BLOSUM62 behaves as expected, so it's probably
some strangeness with the PID distance function when two sequences are
completly unaligned. I'll add it to the bugtrack.

Jim.