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Dear Jalview experts,<div><br></div><div>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. </div><div><br></div><div>Best regards,</div><div><br></div><div>Daron</div><div><br></div><div><span></span></div></body></html>