problems with new jalview


Dear Tisza.

I’ve tracked down the problem, and it is really an issue with MEGA, so I’ve already lodged a bug report with them (I can’t give you a link because the form didn’t give me one, unfortunately).

The error reported by MEGA is because it expects the alignment to be ‘padded’ (that is, every sequence in the alignment file contains only sequence or gap characters, and is the same length).

The workaround is easy. Simply set the ‘Pad Gaps’ option in your Jalview preferences, and your alignments will always be padded to the same length when you edit them. You can also pad an alignment using the ‘pad gaps’ option in the edit menu.


On 15/11/2012 23:17, Geoff Barton wrote:

-------- Original Message --------

Hello Dr. Barton.

I’m a student of Marcela McClures. I just downloaded the latest version of Jalview. I have made some adjustments to my alignment. When I try to put this file into Mega to make trees I get an error, I have attached it. Prior to this version of Jalview I didn’t have any issues moving between the applications. Can you please advise? Marcie asked me to write you directly since there was not contact info on the Jalview website for troubleshooting.

Thank you,

Tisza Bell
PhD Student, Microbiology
Center for Biofilm Engineering
Montana State University

Subject: problems with new jalview
Date: Thu, 15 Nov 2012 16:10:16 -0700
From: Tisza Bell