From birgit.lemcke at systbot.uzh.ch  Tue Dec  9 02:39:33 2008
From: birgit.lemcke at systbot.uzh.ch (Birgit Lemcke)
Date: Tue, 9 Dec 2008 11:39:33 +0100
Subject: [Mesquitelist] Balls and Sticks
Message-ID: <C20E5924-B80A-45B7-8A5C-797A4E695FF6@systbot.uzh.ch>

First of all many thanks for providing and developing Mesquite.

There is something that I wanted to ask about the tree drawing.
I know this is a very personal thing, but I would be extremely happy  
if it would be possibl,e to show the Balls and Sticks Option also with  
a square Tree.
Perhaps it is possible to implement this.
Furthermore I would be interested in calculating correlations of  
discrete data that contains missing values.

Many thanks

Birgit

=============================
Birgit Lemcke
Institut of Systematic Botany
University of Zurich
Zollikerstrasse 107
CH-8008 Z?rich
Switzerland
Ph: +41 (0)44 634 8416		
mail: birgit.lemcke at systbot.uzh.ch	
=============================







From rxl5 at psu.edu  Tue Dec  9 03:22:44 2008
From: rxl5 at psu.edu (Robert E. Loeb)
Date: Tue, 9 Dec 2008 06:22:44 -0500
Subject: [Mesquitelist] A Simple Question
Message-ID: <000c01c959f0$75380b00$5fa82100$@edu>

Colleagues,

 

How do you print in Mesquite?

 

As a novice to Mesquite, does anyone teach an introduction to Mesquite
Course? Is there a Mesquite for Dummies Handbook?

 

Thanks,

Rob

 

Robert Loeb, Ph.D.

 

Kenan Fellow

National Tropical Botanical Gardens

 

Associate Professor of Biology and Forestry

116 Swift Building

Penn State DuBois

College Place

DuBois, PA 15801

814-375-4739

814-375-4724 (FAX)

Personal Web Site:  <http://www.personal.psu.edu/rxl5/>
http://www.personal.psu.edu/rxl5/

 

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From birgit.lemcke at systbot.uzh.ch  Tue Dec  9 03:55:47 2008
From: birgit.lemcke at systbot.uzh.ch (Birgit Lemcke)
Date: Tue, 9 Dec 2008 12:55:47 +0100
Subject: [Mesquitelist] Fwd:  Balls and Sticks
References: <C20E5924-B80A-45B7-8A5C-797A4E695FF6@systbot.uzh.ch>
Message-ID: <B28FB76A-B405-49F4-95F5-99DF4B7A3903@systbot.uzh.ch>

Hello and thousand times sorry.

I just realised that it is possible to do it square.

Sorry gain

Birgit


Anfang der weitergeleiteten E-Mail:

> Von: Birgit Lemcke <birgit.lemcke at systbot.uzh.ch>
> Datum: 9. Dezember 2008 11:39:33 GMT+01:00
> An: MesquiteHelp <mesquitelist at mesquiteproject.org>
> Betreff: [Mesquitelist] Balls and Sticks
>
> First of all many thanks for providing and developing Mesquite.
>
> There is something that I wanted to ask about the tree drawing.
> I know this is a very personal thing, but I would be extremely happy
> if it would be possibl,e to show the Balls and Sticks Option also with
> a square Tree.
> Perhaps it is possible to implement this.
> Furthermore I would be interested in calculating correlations of
> discrete data that contains missing values.
>
> Many thanks
>
> Birgit
>
> =============================
> Birgit Lemcke
> Institut of Systematic Botany
> University of Zurich
> Zollikerstrasse 107
> CH-8008 Z?rich
> Switzerland
> Ph: +41 (0)44 634 8416		
> mail: birgit.lemcke at systbot.uzh.ch	
> =============================
>
>
>
>
>
>
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist

=============================
Birgit Lemcke
Institut of Systematic Botany
University of Zurich
Zollikerstrasse 107
CH-8008 Z?rich
Switzerland
Ph: +41 (0)44 634 8416		
mail: birgit.lemcke at systbot.uzh.ch	
=============================







From rxl5 at psu.edu  Tue Dec  9 07:52:55 2008
From: rxl5 at psu.edu (Robert E. Loeb)
Date: Tue, 9 Dec 2008 10:52:55 -0500
Subject: [Mesquitelist] A Simple Question
In-Reply-To: <5A70F575-77AC-4FA3-99BC-BF9A8280B55A@gmail.com>
References: <000c01c959f0$75380b00$5fa82100$@edu>
	<5A70F575-77AC-4FA3-99BC-BF9A8280B55A@gmail.com>
Message-ID: <002401c95a16$339912e0$9acb38a0$@edu>

Brian,

 

Thanks!

 

I will check this out!

 

Best,

Rob

 

From: Brian O'Meara [mailto:omeara.brian at gmail.com] 
Sent: Tuesday, December 09, 2008 8:25 AM
To: Robert E. Loeb
Cc: Mesquitelist at mesquiteproject.org
Subject: Re: [Mesquitelist] A Simple Question

 

Intro to Mesquite is covered a bit in the Bodega Bay Course in Applied
Phylogenetics (<http://bodegaphylo.wikispot.org/>). 

 

Best,

Brian O'Meara

 

On Dec 9, 2008, at 6:22 AM, Robert E. Loeb wrote:





Colleagues,

 

How do you print in Mesquite?

 

As a novice to Mesquite, does anyone teach an introduction to Mesquite
Course? Is there a Mesquite for Dummies Handbook?

 

Thanks,

Rob

 

Robert Loeb, Ph.D.

 

Kenan Fellow

National Tropical Botanical Gardens

 

Associate Professor of Biology and Forestry

116 Swift Building

Penn State DuBois

College Place

DuBois, PA 15801

814-375-4739

814-375-4724 (FAX)

Personal Web Site:  <http://www.personal.psu.edu/rxl5/>
http://www.personal.psu.edu/rxl5/

 

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

 

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From jschulte at clarkson.edu  Tue Dec  9 08:11:46 2008
From: jschulte at clarkson.edu (James Schulte)
Date: Tue, 9 Dec 2008 11:11:46 -0500
Subject: [Mesquitelist] sampling and resampling
Message-ID: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu>

Hello Mesquite Users,

I have a general inquiry as well as perhaps a specific request for
future versions of Mesquite.

I have a multigene dataset with 7 nuclear genes, all of which are
over 1200 bp and a few between 2-3 kb.  What I would like to do is to
test alternative strategies of data sampling for large multiple
nuclear gene based projects.  That is, is it better to get lots (>10)
of smaller gene fragments (~<700 bp) or use fewer (<10) larger gene
fragments (~>1200) to reconstruct a robustly supported tree for a
particular group.

What I would like to do is to take my dataset with 7 genes and ~11500
bp and rarefy it to make several new datasets that are composed of
difference sized rarefied "genes".  So, for example, I would like to
make 100 new datasets, each 10000 bp that are made up of twenty 500bp
"fragments/gene regions" from the larger dataset.  Or make 100
datasets 10kb that are each made up of five 2000 bp "fragments/gene
regions". At the moment, I can make a single set of 100 datasets with
a "gene" of a particular size using the rarefy option and batch
architecture but what I haven't been able to figure out, and I'm not
sure if Mesquite can do this yet, is if I can easily concatenate
those 100 datasets with 100 other datasets of another "gene".

I hope this is making at least a little bit of sense and I very much
appreciate any advice anyone may have.

Best regards,
Jim


James A. Schulte, II
Department of Biology
177 Clarkson Science Center, MRC 5805
8 Clarkson Avenue
Clarkson University
Potsdam, NY  13699-5805
Phone:  315-268-4401
Fax:  315-268-7118


From wmaddisn at interchange.ubc.ca  Wed Dec 10 17:26:25 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 10 Dec 2008 17:26:25 -0800
Subject: [Mesquitelist] A Simple Question
In-Reply-To: <000c01c959f0$75380b00$5fa82100$@edu>
References: <000c01c959f0$75380b00$5fa82100$@edu>
Message-ID: <a0624080cc5660d46fe7c@[192.168.0.137]>

You can print using the Print items in the file menu.  If you want to 
save the tree to a graphics file, edit that, and then print, you have 
two choices.  You can use the Save Tree as PDF menu item. Or, you can 
ask to Print the tree, and then in the Print dialog box as to save to 
a file.  On Mac OS X, you can ask to save to a PDF.  This actually 
tends to produce better results than the Save Tree as PDF menu item, 
and it's what I use.   On Windows, there is a Print to File option in 
the print dialog, which may or may not save to postscript which can 
be converted to PDF.  Perhaps also there are options to print 
straight to PDF (I'm not fluent in all versions of Windows).

Wayne

At 6:22 AM -0500 9.12.2008, Robert E. Loeb wrote:
>Content-type: multipart/alternative;
>  boundary="Boundary_(ID_wSIQRyqAM8lkeGN0iH/w2Q)"
>Content-language: en-us
>
>Colleagues,
>
>How do you print in Mesquite?
>
>As a novice to Mesquite, does anyone teach an introduction to 
>Mesquite Course? Is there a Mesquite for Dummies Handbook?
>
>Thanks,
>Rob
>
>Robert Loeb, Ph.D.
>
>Kenan Fellow
>National Tropical Botanical Gardens
>
>Associate Professor of Biology and Forestry
>116 Swift Building
>Penn State DuBois
>College Place
>DuBois, PA 15801
>814-375-4739
>814-375-4724 (FAX)
>Personal Web Site: 
><http://www.personal.psu.edu/rxl5/>http://www.personal.psu.edu/rxl5/
>
>
>_______________________________________________
>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 wmaddisn at interchange.ubc.ca  Wed Dec 10 17:26:16 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 10 Dec 2008 17:26:16 -0800
Subject: [Mesquitelist] Fwd:  Balls and Sticks
In-Reply-To: <B28FB76A-B405-49F4-95F5-99DF4B7A3903@systbot.uzh.ch>
References: <C20E5924-B80A-45B7-8A5C-797A4E695FF6@systbot.uzh.ch>
	<B28FB76A-B405-49F4-95F5-99DF4B7A3903@systbot.uzh.ch>
Message-ID: <a0624080bc5660ce5e7f1@[192.168.0.137]>

This isn't an obvious feature, so just to help others find it, here's 
how Birgit did it:

Choose Balls & Sticks as your Tree Form under Drawing.

Then use the Line Style submenu under Drawing.

Wayne


At 12:55 PM +0100 9.12.2008, Birgit Lemcke wrote:
>Hello and thousand times sorry.
>
>I just realised that it is possible to do it square.
>
>Sorry gain
>
>Birgit
>
>
>Anfang der weitergeleiteten E-Mail:
>
>>  Von: Birgit Lemcke <birgit.lemcke at systbot.uzh.ch>
>>  Datum: 9. Dezember 2008 11:39:33 GMT+01:00
>>  An: MesquiteHelp <mesquitelist at mesquiteproject.org>
>>  Betreff: [Mesquitelist] Balls and Sticks
>>
>>  First of all many thanks for providing and developing Mesquite.
>>
>>  There is something that I wanted to ask about the tree drawing.
>>  I know this is a very personal thing, but I would be extremely happy
>>  if it would be possibl,e to show the Balls and Sticks Option also with
>>  a square Tree.
>>  Perhaps it is possible to implement this.
>>  Furthermore I would be interested in calculating correlations of
>>  discrete data that contains missing values.
>>
>>  Many thanks
>>
>>  Birgit
>>
>>  =============================
>>  Birgit Lemcke
>>  Institut of Systematic Botany
>>  University of Zurich
>>  Zollikerstrasse 107
>>  CH-8008 Z?rich
>>  Switzerland
>>  Ph: +41 (0)44 634 8416
>>  mail: birgit.lemcke at systbot.uzh.ch
>>  =============================
>>
>>
>>
>>
>>
>>
>>  _______________________________________________
>>  Mesquitelist mailing list
>>  Mesquitelist at mesquiteproject.org
>>  http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
>=============================
>Birgit Lemcke
>Institut of Systematic Botany
>University of Zurich
>Zollikerstrasse 107
>CH-8008 Z?rich
>Switzerland
>Ph: +41 (0)44 634 8416
>mail: birgit.lemcke at systbot.uzh.ch
>=============================
>
>
>
>
>
>
>_______________________________________________
>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 wmaddisn at interchange.ubc.ca  Wed Dec 10 17:26:31 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 10 Dec 2008 17:26:31 -0800
Subject: [Mesquitelist] sampling and resampling
In-Reply-To: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu>
References: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu>
Message-ID: <a06240812c5661a35069a@[192.168.0.137]>

This could probably done by scripting, but it would be complex.  I'll 
look into the possibility of a new module that could supply a matrix 
that is the concatenation of other matrices, and it would be up to 
you to choose rarefactions for those other matrices.  If it's easy to 
make, then this new module may be available within the next month or 
two.

Wayne

At 11:11 AM -0500 9.12.2008, James Schulte wrote:
>Hello Mesquite Users,
>
>I have a general inquiry as well as perhaps a specific request for
>future versions of Mesquite.
>
>I have a multigene dataset with 7 nuclear genes, all of which are
>over 1200 bp and a few between 2-3 kb.  What I would like to do is to
>test alternative strategies of data sampling for large multiple
>nuclear gene based projects.  That is, is it better to get lots (>10)
>of smaller gene fragments (~<700 bp) or use fewer (<10) larger gene
>fragments (~>1200) to reconstruct a robustly supported tree for a
>particular group.
>
>What I would like to do is to take my dataset with 7 genes and ~11500
>bp and rarefy it to make several new datasets that are composed of
>difference sized rarefied "genes".  So, for example, I would like to
>make 100 new datasets, each 10000 bp that are made up of twenty 500bp
>"fragments/gene regions" from the larger dataset.  Or make 100
>datasets 10kb that are each made up of five 2000 bp "fragments/gene
>regions". At the moment, I can make a single set of 100 datasets with
>a "gene" of a particular size using the rarefy option and batch
>architecture but what I haven't been able to figure out, and I'm not
>sure if Mesquite can do this yet, is if I can easily concatenate
>those 100 datasets with 100 other datasets of another "gene".
>
>I hope this is making at least a little bit of sense and I very much
>appreciate any advice anyone may have.
>
>Best regards,
>Jim
>
>
>James A. Schulte, II
>Department of Biology
>177 Clarkson Science Center, MRC 5805
>8 Clarkson Avenue
>Clarkson University
>Potsdam, NY  13699-5805
>Phone:  315-268-4401
>Fax:  315-268-7118
>
>_______________________________________________
>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 michel.laurin at upmc.fr  Thu Dec 11 00:09:59 2008
From: michel.laurin at upmc.fr (Michel Laurin)
Date: Thu, 11 Dec 2008 09:09:59 +0100
Subject: [Mesquitelist] Simple question about ordering characters
Message-ID: <p06002002c5667a783efd@[192.168.1.4]>

Hello,

	Does anybody know how to order all 
characters of a matrix of discrete characters in 
Mesquite? In MacClade, that could be done from a 
list of characters, but the equivalent list in 
Mesquite gives access to probablitiy models (for 
maximum likelihood analysis), but not ordering 
schemes (for parsimony), apparently. The only way 
I have found is to open a tree, trace each 
character, and then choose ordering. This is not 
ideal, especially if there are many characters.

	Sincerely,

	Michel
-- 
Michel Laurin
CNRS UMR 7179
Universit? Paris 6 - Pierre et Marie Curie
4, place Jussieu
case 19
75005 Paris
FRANCE

tel. (33 1) 44 27 36 92
http://tolweb.org/notes/?note_id=3669

From wmaddisn at interchange.ubc.ca  Thu Dec 11 04:33:44 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Thu, 11 Dec 2008 04:33:44 -0800
Subject: [Mesquitelist] Simple question about ordering characters
In-Reply-To: <p06002002c5667a783efd@[192.168.1.4]>
References: <p06002002c5667a783efd@[192.168.1.4]>
Message-ID: <a06240802c566b8b40552@[192.168.0.137]>

At 9:09 AM +0100 11.12.2008, Michel Laurin wrote:
>Hello,
>
>	Does anybody know how to order all
>characters of a matrix of discrete characters in
>Mesquite? In MacClade, that could be done from a
>list of characters, but the equivalent list in
>Mesquite gives access to probablitiy models (for
>maximum likelihood analysis), but not ordering
>schemes (for parsimony), apparently.

You need to show the column for parsimony models in this List of 
Characters window.  Select Columns>Current Parsimony Models.

Wayne


>The only way
>I have found is to open a tree, trace each
>character, and then choose ordering. This is not
>ideal, especially if there are many characters.
>
>	Sincerely,
>
>	Michel
>--
>Michel Laurin
>CNRS UMR 7179
>Universit? Paris 6 - Pierre et Marie Curie
>4, place Jussieu
>case 19
>75005 Paris
>FRANCE
>
>tel. (33 1) 44 27 36 92
>http://tolweb.org/notes/?note_id=3669
>_______________________________________________
>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 kathleen.miglia at duke.edu  Thu Dec 11 07:19:43 2008
From: kathleen.miglia at duke.edu (Kathleen Miglia)
Date: Thu, 11 Dec 2008 10:19:43 -0500
Subject: [Mesquitelist] Exporting a  Single Tree
Message-ID: <OFFFF15B65.65D7BA00-ON8525751C.00536B04-8525751C.00542F7F@notes.duke.edu>

Hello Mesquiters,

Does anyone know how to export a single tree from a block of trees in 
nexus or newick format? 

Thanks in advance.  Any help with this is greatly appreciated!

Kathleen




Kathleen Miglia, PhD
Molecular Genetics and Microbiology
Duke University Medical Center
234 Jones Research Bldg.
Durham, NC  27710
(919) 668-5260 (Office)
(919) 684-9096 (Lab)
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From wmaddisn at interchange.ubc.ca  Thu Dec 11 07:47:46 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Thu, 11 Dec 2008 07:47:46 -0800
Subject: [Mesquitelist] Exporting a  Single Tree
In-Reply-To: <OFFFF15B65.65D7BA00-ON8525751C.00536B04-8525751C.00542F7F@notes.duke.edu>
References: <OFFFF15B65.65D7BA00-ON8525751C.00536B04-8525751C.00542F7F@notes.duke.edu>
Message-ID: <a06240803c566e596d271@[192.168.0.137]>

The easiest way might be to show the tree in the tree window and 
choose Copy Tree from the Edit menu  Then you can paste it into a 
text editor and save the file.

Otherwise, show the List of Trees for that block, select the row for 
the tree of interest, then select List>Utilities>Extract Selection as 
Tree Block.  Next choose Export from the File menu, and select Export 
NEXUS Tree File or Phylip (trees), then the block of interest.

Wayne

Wayne

>Hello Mesquiters,
>
>Does anyone know how to export a single tree from a block of trees 
>in nexus or newick format?  
>
>Thanks in advance.  Any help with this is greatly appreciated!
>
>Kathleen
>
>
>
>
>Kathleen Miglia, PhD
>Molecular Genetics and Microbiology
>Duke University Medical Center
>234 Jones Research Bldg.
>Durham, NC  27710
>(919) 668-5260 (Office)
>(919) 684-9096 (Lab)
>
>_______________________________________________
>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 wmaddisn at interchange.ubc.ca  Sun Dec 14 21:34:52 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Sun, 14 Dec 2008 21:34:52 -0800
Subject: [Mesquitelist] Export to PDF
In-Reply-To: <491832D8.7000403@gmail.com>
References: <491832D8.7000403@gmail.com>
Message-ID: <a06240807c56b9c7c18a6@[192.168.0.137]>

Sorry, I had missed your note.  Is it possible that the labels are in 
the pdf, but hidden behind a mask or border?    Have you tried 
choosing to print the page, then printing to a file?  That may give 
better results that the direct Save as PDF function.

If you want, email directly to me the pdf that is saved so I can 
understand the issue better.

Wayne


At 11:10 AM -0200 10.11.2008, Alejo wrote:
>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
>_______________________________________________
>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