[Mesquitelist] Request for info from Windows users re. alignment

[David Maddison]

Kip Will reported a problem with some of the alignment tools in 
Mesquite 2.6 running under Windows XP.  I've managed to reproduce the 
Opal OutOfMemoryError, but the other problems running ClustalW and 
Muscle we can't reproduce.

For those of you who have tried to use Clustal or Muscle from within 
Mesquite 2.6, I'd love to hear your successes or failures.  In 
particular, I'd like to know:

- Do these tools (available under the Matrix>Align Multiple Sequences 
submenu) work for you?
- What version of Windows are you running?
- What version of Java have you installed?




>The previous version of Mesquite work without error for ClustalW
>alignments for me. However, since installing 2.6 I haven't been able to
>get any of the alignment programs to run.
>
>For ClustalW and Muscle I get an error message like this--
>"A script refers to a linked file "C:\Documents and Settings\Kipling
>Will\Mesquite_Support_Files\Mesquite_Prefs\temp\temp011f24518e71\ClustalAlign\alignedFile011f2452fbad1402422140.nbrf"
>
>that cannot be found.  Because this linked file cannot be found, the
>remainder of the script might not execute properly, and various warning
>messages might be given.  The probably cause of this is that someone
>saved a file with a second file linked, and then separated the two
>files. To avoid this problem in the future, either unlink files before
>saving, or maintain the linked file in the same relative position (e.g.,
>in the same directory)."
>
>Running Opal gives me this--
>"A command could not be completed because an error occurred (i.e. a
>crash; class java.lang.OutOfMemoryError ). If you save any files, you
>might best use Save As... in case file saving doesn't work properly."
>
>I increased the memory allocation, but no luck. Anyway, it is a modest
>sized matrix so I don't think it is actually a memory issue.
>
>Any helpful suggestions would be appreciated.
>
>Running these...
>-Mesquite 2.6 (build 486)
>-Windows XP 5.1
>-Java 1.6.0_11
>
>kip

-- 

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David R. Maddison
Professor and Curator              PHONE: (520) 621 9781
Department of Entomology           FAX: (520) 621 1150
University of Arizona              email: beetle at ag.arizona.edu
Tucson, AZ 85721   U.S.A.

home page: http://david.bembidion.org
Tree of Life:  http://tolweb.org
Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org

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