From wmaddisn at interchange.ubc.ca  Sun Nov  2 14:26:17 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Sun, 02 Nov 2008 15:26:17 -0700
Subject: [Mesquitelist] two easy questions I hope
In-Reply-To: <alpine.DEB.1.00.0810301845170.16640@sirius.info-ua>
References: <alpine.DEB.1.00.0810301845170.16640@sirius.info-ua>
Message-ID: <a06240804c533d5696fba@[192.168.0.137]>

In any script, there is a current object to which scripting commands 
are being sent.  In your script, it appears that the current object 
is a tree window module.  You need to reset the current object to the 
root Mesquite module itself, so that you can tell Mesquite to quit. 
You reset the current object using the "tell" command.  Thus:

tell Mesquite;
quit;
endTell;

The first line changes the current object to Mesquite itself.

For your second question:  do you want to write the whole text in the 
panel?  At the moment, there isn't a way to do that.  We will enable 
it for the next release.

Wayne


At 7:07 PM +0100 30.10.2008, Gilles HUNAULT wrote:
>Hello everybody.
>
>I am new to Mesquite and I need your help. I have built a lot
>of nexus file and I would like to process them with a linux shell
>script. How do I tell mesquite to quit ? I have tried quit ; and exit ;
>at different locations in the MESQUITE block, but all I get is
>
>Module Tree Window
>(mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker)
>did not respond
>to command quit with arguments ()
>
>or other "employees" telling me the same message.
>
>The second question is how to get the results from Pagel Correlation
>Analysis sent to a file. All I am able to send with saveMessageToFile
>and getLastResultString is to get the last line of the window
>that is, the last p-value only.
>
>Thank you in advance for your help.
>
><<Au plaisir de vous relire.>>
>--
>(.=.)
>Gilles J. HUNAULT, gilles.hunault at univ-angers.fr
>"Science needs culture and feelings"
>http://www.info.univ-angers.fr/pub/gh/
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist


-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416

Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae:  http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html

From lmgc1 at yahoo.com  Wed Nov  5 13:15:18 2008
From: lmgc1 at yahoo.com (Luis Manuel)
Date: Wed, 5 Nov 2008 13:15:18 -0800 (PST)
Subject: [Mesquitelist] Greetings - Help
Message-ID: <801475.33317.qm@web110308.mail.gq1.yahoo.com>

Hello everybody. Someone could help me to obtain the length of branches with any software to include it in the input for the program mesquite.
Does program mesquite calculate the length of branches?

Thank you 
Regards


      

From wmaddisn at interchange.ubc.ca  Thu Nov  6 09:23:27 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Thu, 06 Nov 2008 09:23:27 -0800
Subject: [Mesquitelist] Greetings - Help
In-Reply-To: <801475.33317.qm@web110308.mail.gq1.yahoo.com>
References: <801475.33317.qm@web110308.mail.gq1.yahoo.com>
Message-ID: <a06240809c538d7ca6506@[192.168.0.137]>

Mesquite does not yet have methods to infer branch lengths from 
molecular data, but it can read branch lengths assigned by programs 
such as r8s, BEAST, MrBayes, etc.  Is your question about what 
software to use to obtain branch lengths, or how to read them into 
Mesquite after you have the trees with branch lengths?

Wayne


At 1:15 PM -0800 5.11.2008, Luis Manuel wrote:
>Hello everybody. Someone could help me to obtain the length of 
>branches with any software to include it in the input for the 
>program mesquite.
>Does program mesquite calculate the length of branches?
>
>Thank you
>Regards
>
>
>      
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist


-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416

Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Salticidae:  http://salticidae.org
Tree of Life: http://tolweb.org
Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
Home page: http://salticidae.org/wpm/home.html

From alej.c.s at gmail.com  Mon Nov 10 05:10:48 2008
From: alej.c.s at gmail.com (Alejo)
Date: Mon, 10 Nov 2008 11:10:48 -0200
Subject: [Mesquitelist] Export to PDF
Message-ID: <491832D8.7000403@gmail.com>

Hi all,

    I'm trying to export a tree in character space and some labels are
out of the graph area, so when exporting to pdf some labels are
incomplete. There is a way to fine tunning the final graphs before save 
as pdf? Like
zooming, labels positions, etc?


    Thanks in advance!

    Alejo


-- 
Lic. Alejo C. Scarano
Divisi?n Paleontolog?a Vertebrados
Museo de La Plata
Paseo del bosque s/n
B1900FWA La Plata
Argentina
Tel. 54 221 425-7744/9161 int. 147
Fax 54 221 425-7527
scarano at museo.fcnym.unlp.edu.ar

From s_d_j_brown at hotmail.com  Sat Nov 22 23:04:07 2008
From: s_d_j_brown at hotmail.com (Sam Brown)
Date: Sun, 23 Nov 2008 20:04:07 +1300
Subject: [Mesquitelist] Mesquite and Arlequin
Message-ID: <BAY123-W44CD4A5AB876A9C543EC1D8B090@phx.gbl>


Dear all
 
I downloaded Mequite earlier this year (don't know the version sorry), installed it on my Windows XP powered computer and found it was working very well. A little while later I downloaded Arlequin v 2.000 and loaded that onto the same computer. When that didn't work, I got the Arlequin-Java bundled package, installed that and played around with Arlequin. Now I've come back to Mesquite, which with a warning "Mesquite requires a functioning java installation in order to run". Investigation into the java version installed on the computer reveals that I have Java v. 1.5.
 
I suspect that there is some conflict between Arlequin and Mesquite. Does anyone have any ideas as to what is happening and how I can fix it? 
 
 
Cheers!
 
Sam
 
 
Samuel Brown
Postgraduate Student
Bio-Protection and Ecology Division
PO Box 84
Lincoln University
Lincoln 7647
Canterbury
New Zealand

_________________________________________________________________
Free Windows Live software. Chat, search, share pics and more
http://get.live.com/
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From celestejacq at gmail.com  Mon Nov 24 00:07:12 2008
From: celestejacq at gmail.com (Celeste Jacq)
Date: Mon, 24 Nov 2008 09:07:12 +0100
Subject: [Mesquitelist] Mesquite and Arlequin (Sam Brown)
In-Reply-To: <mailman.1.1227470402.24283.mesquitelist@mesquiteproject.org>
References: <mailman.1.1227470402.24283.mesquitelist@mesquiteproject.org>
Message-ID: <492A60B0.1030102@gmail.com>

That version of Arlequin uses a much-older version of Java than Mesquite uses, that's why you have a problem. Download the newer version of Arlequin (v 3), and then download the up-to-date version of Java and both Arlequin and Mesquite will work fine.


> Dear all
>  
> I downloaded Mequite earlier this year (don't know the version sorry), installed it on my Windows XP powered computer and found it was working very well. A little while later I downloaded Arlequin v 2.000 and loaded that onto the same computer. When that didn't work, I got the Arlequin-Java bundled package, installed that and played around with Arlequin. Now I've come back to Mesquite, which with a warning "Mesquite requires a functioning java installation in order to run". Investigation into the java version installed on the computer reveals that I have Java v. 1.5.
>  
> I suspect that there is some conflict between Arlequin and Mesquite. Does anyone have any ideas as to what is happening and how I can fix it? 
>  
>  
> Cheers!
>  
> Sam
>  
>  
> Samuel Brown
> Postgraduate Student
> Bio-Protection and Ecology Division
> PO Box 84
> Lincoln University
> Lincoln 7647
> Canterbury
> New Zealand
>
> _________________________________________________________________
> Free Windows Live software. Chat, search, share pics and more
> http://get.live.com/
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> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
>
> End of Mesquitelist Digest, Vol 31, Issue 4
> *******************************************
>
>   


From jacoddington at gmail.com  Mon Nov 24 06:36:50 2008
From: jacoddington at gmail.com (Jonathan Coddington)
Date: Mon, 24 Nov 2008 09:36:50 -0500
Subject: [Mesquitelist] Mesquitelist Digest, Vol 31, Issue 4
In-Reply-To: <mailman.1.1227470402.24283.mesquitelist@mesquiteproject.org>
Message-ID: <492abc00.6105be0a.4967.113a@mx.google.com>

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-----Original Message-----
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[mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of
mesquitelist-request at mesquiteproject.org
Sent: Sunday, November 23, 2008 3:00 PM
To: mesquitelist at mesquiteproject.org
Subject: Mesquitelist Digest, Vol 31, Issue 4

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Today's Topics:

   1. Mesquite and Arlequin (Sam Brown)


----------------------------------------------------------------------

Message: 1
Date: Sun, 23 Nov 2008 20:04:07 +1300
From: Sam Brown <s_d_j_brown at hotmail.com>
Subject: [Mesquitelist] Mesquite and Arlequin
To: <mesquitelist at mesquiteproject.org>
Message-ID: <BAY123-W44CD4A5AB876A9C543EC1D8B090 at phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"


Dear all
 
I downloaded Mequite earlier this year (don't know the version sorry),
installed it on my Windows XP powered computer and found it was working very
well. A little while later I downloaded Arlequin v 2.000 and loaded that
onto the same computer. When that didn't work, I got the Arlequin-Java
bundled package, installed that and played around with Arlequin. Now I've
come back to Mesquite, which with a warning "Mesquite requires a functioning
java installation in order to run". Investigation into the java version
installed on the computer reveals that I have Java v. 1.5.
 
I suspect that there is some conflict between Arlequin and Mesquite. Does
anyone have any ideas as to what is happening and how I can fix it? 
 
 
Cheers!
 
Sam
 
 
Samuel Brown
Postgraduate Student
Bio-Protection and Ecology Division
PO Box 84
Lincoln University
Lincoln 7647
Canterbury
New Zealand

_________________________________________________________________
Free Windows Live software. Chat, search, share pics and more
http://get.live.com/
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------------------------------

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Mesquitelist mailing list
Mesquitelist at mesquiteproject.org
http://mesquiteproject.org/mailman/listinfo/mesquitelist


End of Mesquitelist Digest, Vol 31, Issue 4
*******************************************


From peteremidford at yahoo.com  Tue Nov 25 13:25:11 2008
From: peteremidford at yahoo.com (Peter E. Midford)
Date: Tue, 25 Nov 2008 15:25:11 -0600
Subject: [Mesquitelist] PDAP:PDTREE 1.14
Message-ID: <4A15D933-88AB-4481-9975-D97468ED4911@yahoo.com>

I just put a new version of PDAP:PDTREE up on the Mesquite server.  If  
you use PDAP and the Mesquite "phone home" system is working in your  
installation, you should hear (or have heard) about this release when  
you next start Mesquite.  In addition to any difficulties with  
PDAP:PDTREE
itself or the enhancements in this version, I would be interested to  
know if Mesquite did report this new release of PDAP.

Thanks to both Maddisons for bug reports and enhancement suggestions.

Peter

--
Peter Midford
Mesquite Developer





From hulcr at msu.edu  Sun Nov 30 16:50:26 2008
From: hulcr at msu.edu (Jiri Hulcr)
Date: Sun, 30 Nov 2008 16:50:26 -0800
Subject: [Mesquitelist] TNT tree lengths
Message-ID: <305D06028B6646BF8B778A8CDD4717AD@Jiri>

Hi all,
I find Mesquite's ability to communicate with Goloboff's TNT extremely
useful. One thing I haven't been able to figure out is how to import trees
from TNT with branch lengths. I managed to export the branch length tags to
the TNT's tree file, but Mesquite doesn't seem to read the file properly.
Anybody succeeded?
Thanks in advance!
Jiri
 
____________________________________
Jiri Hulcr, PhD
 
Dept. of Entomology, Michigan State University
East Lansing, MI, USA        ph: 517-256-1894
http://www.hisl.ent.msu.edu/people/jiri.php
 
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