From d.a.henk at gmail.com  Tue Oct  7 08:50:15 2008
From: d.a.henk at gmail.com (Daniel)
Date: Tue, 7 Oct 2008 16:50:15 +0100
Subject: [Mesquitelist] scripting associates?
Message-ID: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>

Hello List,

Is there a way to add or set associates without a 'choose'? I'd like to be
able to script many iterations of different associations, but I'm not
finding a very easy way at the moment. Any suggestions would be very
welcome.

Thanks for any help!

-Daniel
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From kathleen.miglia at duke.edu  Tue Oct  7 13:34:04 2008
From: kathleen.miglia at duke.edu (Kathleen Miglia)
Date: Tue, 7 Oct 2008 16:34:04 -0400
Subject: [Mesquitelist] Exporting Sequences as a File in FASTA Format
In-Reply-To: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>
Message-ID: <OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>

Dear Mesquiters,

I have a problem when trying to export sequences from Mesquite as a file 
in FASTA format.  After exporting, I find that all N's are changed to X's, 
even though I changed the missing data symbol from "?" to "N" in Mesquite 
before exporting the sequences.  Does anyone know how to prevent this from 
occurring?

Thanks much,
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 d.a.henk at gmail.com  Tue Oct  7 16:40:22 2008
From: d.a.henk at gmail.com (Daniel)
Date: Wed, 8 Oct 2008 00:40:22 +0100
Subject: [Mesquitelist] scripting associates?
In-Reply-To: <48EB91F9.6050009@cs.rice.edu>
References: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>
	<48EB91F9.6050009@cs.rice.edu>
Message-ID: <4224e620810071640l4289d608o76b5a32ad4542feb@mail.gmail.com>

Thanks very much Cuong, but I think was looking for something else sort
of... and I think I was overly vague.

What I want to do is make different associations based on a simulated matrix
for many matrices, and I'd like to get a score for a tree based on each
association. To write out a new association block from mesquite each time
means I need to figure out how to get mesquite to just write taxon names of
taxa selected based on taxon number because currently I rely on a taxon sort
to determine which taxa belong in each group (this may get more complicated
and be based on some analysis in future, but for now a sort is fine). Maybe
it would be better try manipulating matrices and writing blocks outside of
Mesquite entirely? If the end result was a series of Associaion Blocks that
could be included in a Mesquite Project then scrolled through it would be
perfect.

My current mesquite script takes each simulated dataset or character and
figures out which taxa belong in each group based on a taxa sort or series
of sorts so the taxon numbers assigned to each group remain constant and it
is possible to add associates based on taxon number while the actual taxa
change each iteration. This is ok, but it means I have to click through each
assignment, and that is tedious and can introduce stupid errors. I was
hoping there was something that would let me write the 'choose' part of
assigning associates as arguments.

Still seems a bit vague on my part, but maybe someone has done something
like this already?

thanks tonnes,
Daniel

On Tue, Oct 7, 2008 at 5:44 PM, Cuong Than <cvthan at cs.rice.edu> wrote:

> Hello Daniel,
>
> You can try modifying the the TaxaAssociation block in the NEXUS file,
> something like:
>
> BEGIN TaxaAssociation;
> TITLE gene_in_species;
> TAXA species ,  genes;
> ASSOCIATES
> s1 / g1,
> s2 / g2,
> s3 / g3,
> s4 / g4,
> s5 / g5,
> s6 / g6,
> s7 / g7,
> s8 / g8,
> s9 / g9,
> s10 / g10
> ;
>
> END;
>
> Hope this helps.
>
> Daniel wrote:
>
>> Hello List,
>>  Is there a way to add or set associates without a 'choose'? I'd like to
>> be able to script many iterations of different associations, but I'm not
>> finding a very easy way at the moment. Any suggestions would be very
>> welcome.
>>  Thanks for any help!
>>  -Daniel
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Mesquitelist mailing list
>> Mesquitelist at mesquiteproject.org
>> http://mesquiteproject.org/mailman/listinfo/mesquitelist
>>
>>
>
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From d.a.henk at gmail.com  Tue Oct  7 17:38:47 2008
From: d.a.henk at gmail.com (Daniel)
Date: Wed, 8 Oct 2008 01:38:47 +0100
Subject: [Mesquitelist] Exporting Sequences as a File in FASTA Format
In-Reply-To: <OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>
References: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>
	<OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>
Message-ID: <4224e620810071738ld2e3d24re152b3210052dcc3@mail.gmail.com>

Hi Kathleen,
I think Mesquite is not seeing your Ns as polymorphism or uncertainty
properly. If you have them as A&C&G&T for instance then convert polymorphism
to uncertainty before exporting the matrix I think you'll get Ns rather than
Xs.

good luck,
daniel

On Tue, Oct 7, 2008 at 9:34 PM, Kathleen Miglia <kathleen.miglia at duke.edu>wrote:

>
> Dear Mesquiters,
>
> I have a problem when trying to export sequences from Mesquite as a file in
> FASTA format.  After exporting, I find that all N's are changed to X's, even
> though I changed the missing data symbol from "?" to "N" in Mesquite before
> exporting the sequences.  Does anyone know how to prevent this from
> occurring?
>
> Thanks much,
> 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
>
>
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From kathleen.miglia at duke.edu  Tue Oct  7 18:23:08 2008
From: kathleen.miglia at duke.edu (Kathleen Miglia)
Date: Tue, 7 Oct 2008 21:23:08 -0400
Subject: [Mesquitelist] Exporting Sequences as a File in FASTA Format
In-Reply-To: <4224e620810071738ld2e3d24re152b3210052dcc3@mail.gmail.com>
References: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>	
	<OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>,
	<4224e620810071738ld2e3d24re152b3210052dcc3@mail.gmail.com>
Message-ID: <OF89CA2073.48B86AFE-ON852574DC.0004D5E2-852574DC.00079334@notes.duke.edu>

Thanks very much for your reply, Daniel.
 
I tried what you suggested but the N's were still changed to X's.  I also 
tried "Convert Uncertainties to Polymorphisms" and the same thing 
occurred.  In addition, when I searched for the polymorphic sites that 
were assigned ambiguity codes, I could no longer find them after I 
exported the file.

Kathleen
 
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From d.a.henk at gmail.com  Tue Oct  7 19:04:01 2008
From: d.a.henk at gmail.com (Daniel)
Date: Wed, 8 Oct 2008 03:04:01 +0100
Subject: [Mesquitelist] Exporting Sequences as a File in FASTA Format
In-Reply-To: <OF89CA2073.48B86AFE-ON852574DC.0004D5E2-852574DC.00079334@notes.duke.edu>
References: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>
	<OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>
	<4224e620810071738ld2e3d24re152b3210052dcc3@mail.gmail.com>
	<OF89CA2073.48B86AFE-ON852574DC.0004D5E2-852574DC.00079334@notes.duke.edu>
Message-ID: <4224e620810071904x631c9626t65e49549d9649449@mail.gmail.com>

Sorry it didn't work out easily...
hmmm, when I have a state A&C&G&T then ask Mesquite to convert Polymorphisms
to Uncertainties then ask it to export the matrix as FASTA I get Ns not Xs
and similarly Rs for something coded A&G initially. If you ask mesquite to
convert from Uncertainty to polymorphism and it doesn't give you the A&C&G&T
format for the Ns then it probably isn't seeing them as uncertainties in the
first place. Probably this is something that it must be told to expect.
There are probably lots of little things to check like are ?s or Ns missing
data or is the matrix being read properly to start with?, but maybe the
easiest thing for you is to export it as a different format then pass the
matrices through a conversion external to mesquite.
sorry to really be not much help... maybe I can get back to you later

best,
d

On Wed, Oct 8, 2008 at 2:23 AM, Kathleen Miglia <kathleen.miglia at duke.edu>wrote:

>
> Thanks very much for your reply, Daniel.
>
> I tried what you suggested but the N's were still changed to X's.  I also
> tried "Convert Uncertainties to Polymorphisms" and the same thing occurred.
>  In addition, when I searched for the polymorphic sites that were assigned
> ambiguity codes, I could no longer find them after I exported the file.
>
> Kathleen
>
>
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From beetle at ag.arizona.edu  Wed Oct  8 06:38:03 2008
From: beetle at ag.arizona.edu (David Maddison)
Date: Wed, 8 Oct 2008 06:38:03 -0700
Subject: [Mesquitelist] Exporting Sequences as a File in FASTA Format
In-Reply-To: <OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>
References: <OF0D481CF4.17BD8F54-ON852574DB.006FBF2F-852574DB.0070F249@notes.duke.edu>
Message-ID: <a06240803c512682a1dbc@[192.168.0.197]>

Kathleen,

This is my fault.  I mistakenly used the same missing-data code for 
FASTA DNA sequences as I did for FASTA protein sequences, but the 
former should use N and the later X.  I've fixed this, and the fix 
will appear in the next release of Mesquite.  However, if you can't 
wait, you can download a patch from

http://mesquiteproject.org/FASTAFix.zip

When you unzip this, there will be folders whose names tell you were 
to put the contained items.  You must be using Mesquite 2.5 for this 
to work; don't try it with an earlier version!

Thanks for pointing this out,
David
-- 

===================================================================
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

===================================================================

From lehiggin at uvm.edu  Wed Oct 15 07:17:57 2008
From: lehiggin at uvm.edu (Linden E. Higgins)
Date: Wed, 15 Oct 2008 10:17:57 -0400
Subject: [Mesquitelist] arbitrary branch lengths
Message-ID: <20081015101757.o3pq0mceh1q8kswk@webmail.uvm.edu>

Hi - I just upgraded to the latest version of Mesquite, and discovered  
that some of the branch=length modifications that were in the older  
version appear to have disappeared.  In particular, I was looking for  
the arbitrary models of Grafen, Pagel, and Nee as well as the  
log-transform.  In the prior version, they were listed under "other".   
The manual doesn't describe where these might be, and I was wondering  
if I was missing them or if I needed to construct them from scratch.

Thanks,
Linden

-- 
Linden Higgins
Assistant Research Professor and Lecturer
Department of Biology
University of Vermont
Burlington, VT  05405

phone:  (802) 656-9598

web site:  http//www.uvm.edu/~lehiggin


From peteremidford at yahoo.com  Wed Oct 15 07:52:43 2008
From: peteremidford at yahoo.com (Peter E. Midford)
Date: Wed, 15 Oct 2008 09:52:43 -0500
Subject: [Mesquitelist] arbitrary branch lengths
In-Reply-To: <20081015101757.o3pq0mceh1q8kswk@webmail.uvm.edu>
References: <20081015101757.o3pq0mceh1q8kswk@webmail.uvm.edu>
Message-ID: <48A69A88-9D7C-4C15-9756-09189E0D2C2B@yahoo.com>

Those are in the PDAP package.  You will need to download the latest  
version of PDAP to use it with Mesquite 2.5.

Hope this helps,

Peter

On Oct 15, 2008, at 9:17, Linden E. Higgins wrote:

> Hi - I just upgraded to the latest version of Mesquite, and discovered
> that some of the branch=length modifications that were in the older
> version appear to have disappeared.  In particular, I was looking for
> the arbitrary models of Grafen, Pagel, and Nee as well as the
> log-transform.  In the prior version, they were listed under "other".
> The manual doesn't describe where these might be, and I was wondering
> if I was missing them or if I needed to construct them from scratch.
>
> Thanks,
> Linden
>
> -- 
> Linden Higgins
> Assistant Research Professor and Lecturer
> Department of Biology
> University of Vermont
> Burlington, VT  05405
>
> phone:  (802) 656-9598
>
> web site:  http//www.uvm.edu/~lehiggin
>
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist

--
Peter Midford
Mesquite Developer





From jonah.choiniere at gmail.com  Mon Oct 20 11:09:12 2008
From: jonah.choiniere at gmail.com (Jonah Choiniere)
Date: Mon, 20 Oct 2008 14:09:12 -0400
Subject: [Mesquitelist] Ghost lineages in Mesquite
Message-ID: <b90157510810201109u3a2f35d6n39ac861e3ce7c47a@mail.gmail.com>

Hello all,

I've downloaded the stratigraphic add-ons for Mesquite 2.5 by Laurin et al, but
reluctantly they do not contain techniques for calculating or
displaying ghost lineages. Has anyone had luck working with these
add-ons and ghost lineages? Are there any software platforms out there
that interact well with Mesquite and allow these calculations?

Thank you.

Sincerely,
Jonah


-- 
Jonah Choiniere
Ph.D. Candidate
The George Washington University
Robert Weintraub Program in Systematics and Evolution

From jonah.choiniere at gmail.com  Mon Oct 20 11:09:45 2008
From: jonah.choiniere at gmail.com (Jonah Choiniere)
Date: Mon, 20 Oct 2008 14:09:45 -0400
Subject: [Mesquitelist] Simulating "morphological" characters
Message-ID: <b90157510810201109m729c5269sd1c5dcf3da63294@mail.gmail.com>

Hello again,

My second question this week concerns the simulation of
"morphological"-type data in Mesquite. While I realize that 4 states
(A-C-T-G) are no different operationally than two states
(absence/presence), I would like to run some simulation studies for a
more paleontological audience and felt that data simulated under a
more familiar framework would be more appropriate. Is there a way to
simulate the evolution of 2-state characters on a tree in Mesquite?

Sincerely,
Jonah
Jonah Choiniere
Ph.D. Candidate
The George Washington University
Robert Weintraub Program in Systematics and Evolution

From michel.laurin at upmc.fr  Mon Oct 20 13:06:40 2008
From: michel.laurin at upmc.fr (Michel Laurin)
Date: Mon, 20 Oct 2008 22:06:40 +0200
Subject: [Mesquitelist] Ghost lineages in Mesquite
In-Reply-To: <b90157510810201109u3a2f35d6n39ac861e3ce7c47a@mail.gmail.com>
References: <b90157510810201109u3a2f35d6n39ac861e3ce7c47a@mail.gmail.com>
Message-ID: <p06002000c52294c00c06@[192.168.1.2]>

Hello Jonah,

	The Stratigraphic Tools and StratAdds 
don't compute ghost lineages, so far (sorry). 
That would be a nice addition, but right now, I 
don't have time to work on this. I have used 
Ghost to compute this and to test for statistical 
significance of the stratigraphic fit (I can send 
you a paper if you want to know more about this).

	Sincerely,

	Michel

>Hello all,
>
>I've downloaded the stratigraphic add-ons for 
>Mesquite 2.5 by Laurin et al, but
>reluctantly they do not contain techniques for calculating or
>displaying ghost lineages. Has anyone had luck working with these
>add-ons and ghost lineages? Are there any software platforms out there
>that interact well with Mesquite and allow these calculations?
>
>Thank you.
>
>Sincerely,
>Jonah
>
>
>--
>Jonah Choiniere
>Ph.D. Candidate
>The George Washington University
>Robert Weintraub Program in Systematics and Evolution
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist


-- 
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 adiape at cantv.net  Tue Oct 21 01:44:41 2008
From: adiape at cantv.net (Antonio Diaz)
Date: Tue, 21 Oct 2008 04:14:41 -0430
Subject: [Mesquitelist] rooting simultaed gene trees
Message-ID: <381-220081022184441277@cantv.net>

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From Christy.Hipsley at MUSEUM.HU-Berlin.de  Mon Oct 27 08:39:18 2008
From: Christy.Hipsley at MUSEUM.HU-Berlin.de (Hipsley, Christy)
Date: Mon, 27 Oct 2008 16:39:18 +0100
Subject: [Mesquitelist] drawing SD bars in Mesquite
Message-ID: <DA7DFE7720AEDD44AE6E24A028A267EE0101FDAC@museum08mem.naturkundemuseum-berlin.de>

Can anyone please tell me how to enter posterior date ranges onto a phylogenetic tree in Mesquite? 
I started with a nexus file and managed to draw an ultrametric tree with a timescale, but cannot figure out how to draw in bars showing standard deviations at each node.


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From wmaddisn at interchange.ubc.ca  Wed Oct 29 22:09:58 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 29 Oct 2008 22:09:58 -0700
Subject: [Mesquitelist] scripting associates?
In-Reply-To: <4224e620810071640l4289d608o76b5a32ad4542feb@mail.gmail.com>
References: <4224e620810070850l6862cabeo2a63ea08940f7360@mail.gmail.com>
	<48EB91F9.6050009@cs.rice.edu>
	<4224e620810071640l4289d608o76b5a32ad4542feb@mail.gmail.com>
Message-ID: <a06240835c52ed91495df@[192.168.0.159]>

You can't yet do what you want.  You can create new association 
blocks, but you can't set the associations by scripting.  However, 
I've just programmed that ability into Mesquite, and so when the next 
update comes out, you'll be able to do it.

What you can do now is as follows.  Set up a file with two taxa 
blocks.  Then go to any window for that file, and choose Send Script 
from the Scripting submenu of the Window menu.  Paste in:

getFileCoordinator;
tell It;
getEmployee '#mesquite.assoc.ManageAssociations.ManageAssociations';
tell It;
	makeAssociation 0 1;
endTell;
endTell;

And hit "OK".  The association block is made, but it doesn't contain 
anything interesting.  In the next update, this is what you'd enter:

getFileCoordinator;
tell It;
getEmployee '#mesquite.assoc.ManageAssociations.ManageAssociations';
tell It;
	makeAssociation 0 1;
	Object.assoc *it;
	tell *Object.assoc;
		associate 0 0;
		associate 0 1;
		associate 1 5;
		associate 1 4; [to associate taxon 0 in block 0 with 
taxon 4 in block 1]
		associate 2 2;
		associate 2 3;
	endTell;
endTell;
endTell;

Wayne

At 12:40 AM +0100 8.10.2008, Daniel wrote:
>Thanks very much Cuong, but I think was looking for something else 
>sort of... and I think I was overly vague.
>
>What I want to do is make different associations based on a 
>simulated matrix for many matrices, and I'd like to get a score for 
>a tree based on each association. To write out a new association 
>block from mesquite each time means I need to figure out how to get 
>mesquite to just write taxon names of taxa selected based on taxon 
>number because currently I rely on a taxon sort to determine which 
>taxa belong in each group (this may get more complicated and be 
>based on some analysis in future, but for now a sort is fine). Maybe 
>it would be better try manipulating matrices and writing blocks 
>outside of Mesquite entirely? If the end result was a series of 
>Associaion Blocks that could be included in a Mesquite Project then 
>scrolled through it would be perfect.
>
>My current mesquite script takes each simulated dataset or character 
>and figures out which taxa belong in each group based on a taxa sort 
>or series of sorts so the taxon numbers assigned to each group 
>remain constant and it is possible to add associates based on taxon 
>number while the actual taxa change each iteration. This is ok, but 
>it means I have to click through each assignment, and that is 
>tedious and can introduce stupid errors. I was hoping there was 
>something that would let me write the 'choose' part of assigning 
>associates as arguments.
>
>Still seems a bit vague on my part, but maybe someone has done 
>something like this already?
>
>thanks tonnes,
>Daniel
>
>On Tue, Oct 7, 2008 at 5:44 PM, Cuong Than 
><<mailto:cvthan at cs.rice.edu>cvthan at cs.rice.edu> wrote:
>
>Hello Daniel,
>
>You can try modifying the the TaxaAssociation block in the NEXUS 
>file, something like:
>
>BEGIN TaxaAssociation;
>TITLE gene_in_species;
>TAXA species ,  genes;
>ASSOCIATES
>s1 / g1,
>s2 / g2,
>s3 / g3,
>s4 / g4,
>s5 / g5,
>s6 / g6,
>s7 / g7,
>s8 / g8,
>s9 / g9,
>s10 / g10
>;
>
>END;
>
>Hope this helps.
>
>Daniel wrote:
>
>Hello List,
>  Is there a way to add or set associates without a 'choose'? I'd 
>like to be able to script many iterations of different associations, 
>but I'm not finding a very easy way at the moment. Any suggestions 
>would be very welcome.
>  Thanks for any help!
>  -Daniel
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Mesquitelist mailing list
><mailto:Mesquitelist at mesquiteproject.org>Mesquitelist at mesquiteproject.org
><http://mesquiteproject.org/mailman/listinfo/mesquitelist>http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
>
>
>
>_______________________________________________
>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 Oct 29 22:10:12 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 29 Oct 2008 22:10:12 -0700
Subject: [Mesquitelist] Simulating "morphological" characters
In-Reply-To: <b90157510810201109m729c5269sd1c5dcf3da63294@mail.gmail.com>
References: <b90157510810201109m729c5269sd1c5dcf3da63294@mail.gmail.com>
Message-ID: <a06240839c52ee58a6e8e@[192.168.0.159]>

Yes, if you first create either an Mk1 model or an AsymmMk model.  See:

http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/RandomSimul/simChars.html#simulations

When you choose to simulate a matrix or individual characters, select 
"Evolve Categorical Characters" as the simulator and then your model.

There are many contexts in which you can simulate characters, for 
instance for any calculations that take characters as input.  You can 
simulate a series of characters on a single tree, or one character on 
each of many trees, and so on.  For example, if you want to simulate 
a whole matrix of characters that you can look at and edit, have a 
tree window open showing the tree on which to simulate, then choose 
Characters>Make New Matrix From>Simulated Matrices on Current Tree, 
then continue from there.

Wayne


At 2:09 PM -0400 20.10.2008, Jonah Choiniere wrote:
>Hello again,
>
>My second question this week concerns the simulation of
>"morphological"-type data in Mesquite. While I realize that 4 states
>(A-C-T-G) are no different operationally than two states
>(absence/presence), I would like to run some simulation studies for a
>more paleontological audience and felt that data simulated under a
>more familiar framework would be more appropriate. Is there a way to
>simulate the evolution of 2-state characters on a tree in Mesquite?
>
>Sincerely,
>Jonah
>Jonah Choiniere
>Ph.D. Candidate
>The George Washington University
>Robert Weintraub Program in Systematics and Evolution
>_______________________________________________
>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 Oct 29 22:10:23 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 29 Oct 2008 22:10:23 -0700
Subject: [Mesquitelist] rooting simultaed gene trees
In-Reply-To: <381-220081022184441277@cantv.net>
References: <381-220081022184441277@cantv.net>
Message-ID: <a0624083ac52ee796e971@[192.168.0.159]>

At 4:14 AM -0430 21.10.2008, Antonio Diaz wrote:
>Dear all,
>
>
>
>I need your helpful advices. I am testing several speciation 
>hypothesis based on four closely related oceanic species. Genetrees 
>were simulated under each hypothesis using an evolutionary 
>character model that adjusts to observed level of diveregence among 
>lineages. I would like to test if deep coalescence of estimated 
>genetree (throug maximum likelihood) fit into the distribution of 
>deep coalescences of simulated gene trees.
>
>The specific questions are:
>
>How can I root the simulated genetrees according to a predefined 
>species tree hypothesis?

I'm not sure exactly what you mean by this.  Mesquite can choose the 
rooting of the gene tree that minimizes deep coalescences within a 
given species tree, if the "Treat contained as unrooted" option is 
chosen.  Is that what you mean?

>  Given that some lineages in some genetrees are not monophyletic, 
>which haplotype (lineage) within the most ancestral species should I 
>take as the root?

You know the roots of your simulated trees.  However, if your 
estimated gene trees are unrooted, then it would be best to treat the 
simulated trees also as unrooted.  You can do "forget" the roots of 
the simulated trees when you measure their deep coalescence fit into 
the species tree by selecting the "Treat contained as unrooted" menu 
item.

>
>
>
>Is it correct that the estimated genetree be set as unrooted, 
>although previous results (networks and outgroups) suggest that some 
>haplotypes are most ancestral?


If your estimated gene tree is rooted, then you could choose to treat 
the simulated gene trees as rooted. However, this would not take into 
account error on the rooting of the estimated gene tree.

Does this help?

Wayne


>
>
>
>Thank you very much
>
>
>
>Warm Regards
>
>
>
>Antonio
>
>
>
>
>_______________________________________________
>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 Oct 29 22:10:39 2008
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 29 Oct 2008 22:10:39 -0700
Subject: [Mesquitelist] drawing SD bars in Mesquite
In-Reply-To: <DA7DFE7720AEDD44AE6E24A028A267EE0101FDAC@museum08mem.naturkundemuseum-be
	rlin.de>
References: <DA7DFE7720AEDD44AE6E24A028A267EE0101FDAC@museum08mem.naturkundemuseum-be
	rlin.de>
Message-ID: <a0624083dc52ef146a276@[192.168.0.159]>

At 4:39 PM +0100 27.10.2008, Hipsley, Christy wrote:
>
>Can anyone please tell me how to enter posterior date ranges onto a 
>phylogenetic tree in Mesquite?
>I started with a nexus file and managed to draw an ultrametric tree 
>with a timescale, but cannot figure out how to draw in bars showing 
>standard deviations at each node.

There is not yet a facility to do that.  We are planning however some 
functions to summarize node ages over trees.  Is your goal to 
summarize node ages over a series of trees from BEAST, for example?

Wayne

>
>
>
>_______________________________________________
>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 gilles.hunault at univ-angers.fr  Thu Oct 30 11:07:09 2008
From: gilles.hunault at univ-angers.fr (Gilles HUNAULT)
Date: Thu, 30 Oct 2008 19:07:09 +0100 (CET)
Subject: [Mesquitelist] two easy questions I hope
Message-ID: <alpine.DEB.1.00.0810301845170.16640@sirius.info-ua>


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/