Hello John.

I'm very glad to hear that Jalview is working better now - we'll add
something to the FAQ ( about reinstalling.

Now, your two questions:

- DNA Editing. Unfortunately, we were focusing on the amino-acid
support for jalview in this release. One of the priorities for the next
is to handle DNA sensibly - the algorithms used in Jalview for property
conservation and quality all use amino acid substitution measures,
rather than base substitutions.

- Selecting and Editing. You now have to press control whilst
click+dragging the mouse to edit the alignment - this is the biggest
change from the old release. If you check the help documentation
(JalviewDesktop->Help->Documentation) there's a summary of the new
editing features. There's also a quick-reference card on the website

Hopefully you'll get used to these differences between the old and the
new jalview. However - I also checked up on BioEdit for linux. As you
said, there's no explicit support, but I did find a mention of someone
having run it through wine (the Windows Emulator):

happy Jalviewing!


On 23 Jun 2005 15:15:10 -0700 John Taylor <> wrote:

Hi Jim,

We reinstalled Jalview and it seems to be working now. But, two things
are causing us trouble. First, how do we tell the program that we're
looking at DNA and not an amino acid alignment? When we mouse over an A
it thinks it's an alanine. Also, editing is a problem. We're supposed
to be able to select a residue and then drag it to the left or right.
But all that seems to happen is that the residue on the left or right
get highlighted too. Nothing moves. Maybe we're not selecting it

I've been looking for a BioEdit for Linux for a while and this seems to
be it. But, the keyboard-based editing on BioEdit seems a lot easier.
Maybe we just need some time.



On Thu, 2005-06-23 at 02:07, Jim Procter wrote:
> Hello John - I'm sorry to hear your having problems with Jalview.
> The error you have seems to be due to Jalview not recognising the type
> of a file it is trying to load in - but that doesn't fit with your
> description of how you ran Jalview.
> We will check out the InstallAnywhere+VM installation for RH8, but in
> the meantime, could you check the following:
> - make sure you've got the latest version of jalview
> - Version 2 came out last friday.
> and we are not supporting the old Jalview anymore
> - if you download a new version, you should completely remove
> the old installAnywhere version first.
> You'll like the new version - its a little different but has all the features!
> Jim Procter.
> ---------------------------------------------------------------------
> J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
> Phone: +44 (0)1382 348734
> On Wed, 22 Jun 2005 14:53:17 -0700 > > John Taylor <> wrote:
> > Dear Jalview,
> >
> > This (below) is the error message I get when I type Jalview after the
> > installation. It, the program, starts up properly after the
> > installation, but after exiting, I cannot restart the program from the
> > command line. We're running Linux RH8.0. It was installed with
> > InstallAnywhere with JavaVM.
> >
> > Thanks,
> >
> > John Taylor
> > University of Victoria
> >
> > john@crick john]$ Jalview
> > In FormatAdapter
> > java.lang.NullPointerException
> > Exception in thread "main" java.lang.NullPointerException
> > at jalview.AlignFrame.main(
> >
> >

J. B. Procter (VAMSAS Project) Barton Bioinformatics Research Group
Phone: +44 (0)1382 348734