[Biojava-l] Multiple Sequence Alignment - Limits?

Hannes Brandstätter-Müller biojava at hannes.oib.com
Wed Oct 19 04:36:19 UTC 2011

Hi Andreas,

I will try that later today if that makes any difference; I ran a
larger alignment batch overnight, and I noticed that this limit seems
to have been a coincidence; HOWEVER, the aligned sequences are always
not as many as the input sequences, is this caused by memory
constraints or how can I influence that?


On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Hannes,
> did you try to increase memory settings for your JVM?  e.g. -Xmx500M
> Andreas
> On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandstätter-Müller
> <biojava at hannes.oib.com> wrote:
>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandstätter-Müller
>> <biojava at hannes.oib.com> wrote:
>>> Hi again!
>>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>>> that there seems to be a limit of 132 Sequences that are present in
>>> the final alignment - is this some kind of hardcoded limit, or can I
>>> work around that somehow?
>>> Hannes
>> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> fasta format. Is there a way to work around that limit?
>> Hannes
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