Hi Cricket.. and Mungo.

Interesting thread !  I just wanted to add a couple of hints:

On 20/09/2016 14:05, Mungo Carstairs (Staff) wrote:
> For the memory issue, can you try higher max heap sizes e.g. 2000m?

If you have javaws on your path, then try this:

Assuming you have openjdk 1.8 or later, then you should be able to
change '15G' to *just under* your machine's physical memory - ie 100G,
if I read your 'swap -mh' output right.

The 'version=Develop' means you'll be launching the development version,
which will basically be version 2.10 of Jalview when we release it in
the next week or so. I'd recommend using this version, since we've been
optimising Jalview so it works better with genomic data.

> file in its own separate window. However, each contig is listed as what
> looks like a new sequence that can be aligned rather than as a single
> fasta file (containing multiple contigs). 
Yes. Most draft assemblies look like this !

I did do a multi-fasta file
> alignment (to the reference) using Mauve, but when I try to look at the
> alignment file in Jalview, I get the memory error, and all of the
> contigs are still there.

Presumably Mauve produced a single fasta or GFF3 output file ?  It is
this file you should try to read in to Jalview.

Just a final word - Jalview really works best for analysing loci - so if
you have any putative CDS annotation, you probably want to import them, too.

Let us know how you get on !
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