[Jalview-discuss] max file size

[Jim Procter]

On 26/03/2012 17:23, Jessie Richer wrote:
> Is there a maximum file size (fasta format) that Jalview will accept? 
> If so, what is it? I cant increase java/virtual memory - no access to 
> this at my university. So curious to know what the max file size is 
> for running alignments on the "launch anywhere" downloadable version 
> of Jalview.
By 'Launch anywhere' I assume you mean the webstart version ?  If so, 
you can tweak virtual memory settings by creating a custom JNLP file 
(http://www.jalview.org/jvmmemoryparams.html).
If you mean the 'InstallAnywhere version' then you may indeed have 
problems due to admin rights.

Either way, the largest memory allocation you can set is around 50% of 
the physical memory of your machine (e.g. if you have 2G memory, then 
you can allocate up to around 1G to Jalview).
>
> Finishing up my co-op and want to know if I can align a HUGE file, (i 
> dont know what size it would be yet since I have not made it). 
> Basically looking to make a neigbour joining tree in jalview with 
> about 15 different species (ranging from 10 sequences for one species 
> up to about 800 for another). Dont want to waste my time making this 
> huge file if it wont align/run.
>
You aren't going to be able to align that many sequences with the public 
web services that Jalview talks to, since there is a physical limit of 
1000 sequences of up to 1000 residues each. Tree building will probably 
take a long time once you've computed that alignment, too, since Jalview 
doesn't use any tricks like BioNJ to speed up the tree building process. 
Basically, for very large sequence sets, there are a couple of routes, 
and all involve downloading and installing additional programs which 
have to be configured or run from the command line. Email me directly if 
you'd like to discuss your options - since they don't necessarily 
involve Jalview ;)

Jim.

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