From michel.laurin at upmc.fr  Sat Jan  3 08:15:18 2009
From: michel.laurin at upmc.fr (Michel Laurin)
Date: Sat, 3 Jan 2009 17:15:18 +0100
Subject: [Mesquitelist] Question on diagnostic checks in PDAP
Message-ID: <p06002000c5853e6d7396@[192.168.1.2]>

Happy New Year to all of you,

	I just noticed that when checking 
diagnostics to make sure that there are no 
statistical artefacts (that the contrasts are 
adquately standardized), the PDAP module of 
Mesquite removes one more degree of freedom than 
when doing contrast analysis. For instance, for a 
fully-resolved tree of 26 taxa, when doing 
contrasts, 25 df are left, but for the diagnostic 
checks, only 24 appear to be left. Why is that? 
Is there a way, for large matrices, to check 
quickly how may characters show statistical 
artefacts? I have several matrices of 250 
characters each, and I don't really want to have 
to scroll back and forth between graphic view and 
text view (the graphic view being necessary to 
scroll between characters, and the text view, to 
see the probabilities). Any help would be welcome.

	Sincerely,

	Michel
-- 
Michel Laurin
UMR CNRS 5143 "Centre de Recherches sur la 
Pal?obiodiversit? et les Pal?oenvironnements"
Mus?um National d'Histoire Naturelle
D?partement Histoire de la Terre
B?timent de G?ologie
Case Postale 48
57 rue Cuvier
F-75231 PARIS Cedex 05
FRANCE
tel. (33 1) 44 27 36 92
http://tolweb.org/notes/?note_id=3669

From tgarland at ucr.edu  Sat Jan  3 08:54:34 2009
From: tgarland at ucr.edu (tgarland at ucr.edu)
Date: Sat,  3 Jan 2009 08:54:34 -0800 (PST)
Subject: [Mesquitelist] Question on diagnostic checks in PDAP
Message-ID: <20090103085434.ALN06584@fmh.ucr.edu>

The extra degree of freedom gone in the diagnostic graphs is
correct because the correlation of the absolute value of
standardized contrasts (Y) versus their standard deviations
(X) is NOT computed through the origin (because they are absolute
values).  See this paper:
 
Garland, T., Jr., P. H. Harvey, and A. R. Ives. 1992.
Procedures for the analysis of comparative data using
phylogenetically independent contrasts.
Systematic Biology 41:18-32.

This is essentially the ONLY situation with contrasts where the computations are not done through the origin.

Cheers,
Ted

Theodore Garland, Jr., Ph.D.
Professor
Department of Biology
University of California
Riverside, CA 92521
Phone:  (951) 827-3524 = Ted's office (with answering machine)
Phone:  (951) 827-5724 = Ted's lab
Phone:  (951) 827-5903 = Dept. office
Home Phone:  (951) 328-0820
FAX:  (951) 827-4286 = Dept. office
Email:  tgarland at ucr.edu
http://biology.ucr.edu/people/faculty/Garland.html
List of all publications with PDF files:
http://biology.ucr.edu/people/faculty/Garland/GarlandPublications.html
Associate Director
Network for Experimental Research on Evolution
http://nere.bio.uci.edu/
(A University of California Multicampus Research Project)



  ---- Original message ----

    Date: Sat, 3 Jan 2009 17:15:18 +0100
    From: Michel Laurin <michel.laurin at upmc.fr>
    Subject: [Mesquitelist] Question on diagnostic checks in
    PDAP
    To: Mesquite list <mesquitelist at mesquiteproject.org>

    >Happy New Year to all of you,
    >
    > I just noticed that when checking
    >diagnostics to make sure that there are no
    >statistical artefacts (that the contrasts are
    >adquately standardized), the PDAP module of
    >Mesquite removes one more degree of freedom than
    >when doing contrast analysis. For instance, for a
    >fully-resolved tree of 26 taxa, when doing
    >contrasts, 25 df are left, but for the diagnostic
    >checks, only 24 appear to be left. Why is that?
    >Is there a way, for large matrices, to check
    >quickly how may characters show statistical
    >artefacts? I have several matrices of 250
    >characters each, and I don't really want to have
    >to scroll back and forth between graphic view and
    >text view (the graphic view being necessary to
    >scroll between characters, and the text view, to
    >see the probabilities). Any help would be welcome.
    >
    > Sincerely,
    >
    > Michel
    >--
    >Michel Laurin
    >UMR CNRS 5143 "Centre de Recherches sur la
    >Pal?obiodiversit? et les Pal?oenvironnements"
    >Mus?um National d'Histoire Naturelle
    >D?partement Histoire de la Terre
    >B?timent de G?ologie
    >Case Postale 48
    >57 rue Cuvier
    >F-75231 PARIS Cedex 05
    >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

From wmaddisn at interchange.ubc.ca  Thu Jan  8 22:17:11 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Thu, 08 Jan 2009 22:17:11 -0800
Subject: [Mesquitelist] Mesquite 2.6 Beta
In-Reply-To: <p06002000c5853e6d7396@[192.168.1.2]>
References: <p06002000c5853e6d7396@[192.168.1.2]>
Message-ID: <a06240801c58c9aff055b@[192.168.0.197]>

We're looking for volunteers to try out a beta version of Mesquite 
2.6.  It's available at:

http://mesquiteproject.org/MesquiteBeta

Among the new features is an option to simplify the interface by 
hiding menu items and tools you might not be likely to use.  There 
are some built-in simplification themes (e.g., MacClade-like; 
population genetics; etc.), and you can build your own.  You might 
find this especially useful for teaching courses.

We're hoping to release version 2.6 over the next two weeks.  We'd 
very much appreciate feedback as to how well the beta version works 
for you.


-- 
-------------------------------------------------------------------
Wayne Maddison                        David R. Maddison
Departments of Zoology and Botany     Department of Entomology
University of British Columbia        University of Arizona
Vancouver, BC   V6T 1Z4               Tucson, AZ   85721
email: wmaddisn at interchange.ubc.ca    email: beetle at ag.arizona.edu

Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Tree of Life: http://tolweb.org

From hulcr at msu.edu  Sun Jan 11 13:10:26 2009
From: hulcr at msu.edu (Jiri Hulcr)
Date: Sun, 11 Jan 2009 13:10:26 -0800
Subject: [Mesquitelist] pairwise between-taxa distances
Message-ID: <2DBE2C5292B846C3B2F882084C790F02@Jiri>

Hi,
Would anyone help me figure out how I can get a list of pairwise distances
between taxa in Mesquite? It is simple to get the scattergram for all
pairwise distances, or the underlying list of numbers, but I need the
information for each pair of taxa. For example, I need a list with three
columns, Taxon1, Taxon2, Distance. I am interested in simple patristic
distances implied by the tree for morphological data, or molecular distances
using a sequence matrix, a tree and a model. Is it possible in Mesquite?
Thanks in advance!
Jiri
 
 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090111/6e4001fb/attachment.html 

From michel.laurin at upmc.fr  Sun Jan 11 23:34:42 2009
From: michel.laurin at upmc.fr (Michel Laurin)
Date: Mon, 12 Jan 2009 08:34:42 +0100
Subject: [Mesquitelist] pairwise between-taxa distances
In-Reply-To: <2DBE2C5292B846C3B2F882084C790F02@Jiri>
References: <2DBE2C5292B846C3B2F882084C790F02@Jiri>
Message-ID: <p06002000c590a14ff1c8@[192.168.1.2]>

Hi Jiri,

	If your tree reflects the distances you 
want to get, you can export a phylogenetic 
distance matrix between all pairs of taxa (not 
only taxa 1 and 2) of a tree from Mesquite, if 
you have installed my optional Stratigraphic 
Tools (available from the main Mesquite page, 
http://mesquiteproject.org/mesquite/mesquite.html). 
Once installed, the option is available, if a 
Tree window is active (on front). Just go to the 
Tree menu, Utilities submenu, and select "Export 
tree in distance matrix format". A dialog box 
will then prompt you for the name and location of 
the tab-delimited text file which will include 
the matrix. It can then easily be imported into 
Excel or various other standard problems 
(including R, for principal coordinate analysis). 
If you need more information, I suggest you 
contact me off the list.

	Sincerely,

	Michel

>Hi,
>Would anyone help me figure out how I can get a 
>list of pairwise distances between taxa in 
>Mesquite? It is simple to get the scattergram 
>for all pairwise distances, or the underlying 
>list of numbers, but I need the information for 
>each pair of taxa. For example, I need a list 
>with three columns, Taxon1, Taxon2, Distance. I 
>am interested in simple patristic distances 
>implied by the tree for morphological data, or 
>molecular distances using a sequence matrix, a 
>tree and a model. Is it possible in Mesquite?
>Thanks in advance!
>Jiri
>
>
>
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist


-- 
Michel Laurin
UMR CNRS 5143 "Centre de Recherches sur la 
Pal?obiodiversit? et les Pal?oenvironnements"
Mus?um National d'Histoire Naturelle
D?partement Histoire de la Terre
B?timent de G?ologie
Case Postale 48
57 rue Cuvier
F-75231 PARIS Cedex 05
FRANCE
tel. (33 1) 44 27 36 92
http://tolweb.org/notes/?note_id=3669
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090112/03a9e502/attachment.html 

From wmaddisn at interchange.ubc.ca  Wed Jan 14 11:19:22 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Wed, 14 Jan 2009 11:19:22 -0800
Subject: [Mesquitelist] pairwise between-taxa distances
In-Reply-To: <p06002000c590a14ff1c8@[192.168.1.2]>
References: <2DBE2C5292B846C3B2F882084C790F02@Jiri>
	<p06002000c590a14ff1c8@[192.168.1.2]>
Message-ID: <a06240802c593ea9aee6f@[137.82.80.142]>

The next release of Mesquite (coming soon) will have a new module to 
export taxa distances.  With this you can export not only patristic 
distances, but other distances as well (e.g., pairwise distances from 
sequence data, geographic distances if using Cartographer).

Wayne


At 8:34 AM +0100 12.1.2009, Michel Laurin wrote:
>Hi Jiri,
>
>	If your tree reflects the distances you want to get, you can 
>export a phylogenetic distance matrix between all pairs of taxa (not 
>only taxa 1 and 2) of a tree from Mesquite, if you have installed my 
>optional Stratigraphic Tools (available from the main Mesquite page, 
>http://mesquiteproject.org/mesquite/mesquite.html). Once installed, 
>the option is available, if a Tree window is active (on front). Just 
>go to the Tree menu, Utilities submenu, and select "Export tree in 
>distance matrix format". A dialog box will then prompt you for the 
>name and location of the tab-delimited text file which will include 
>the matrix. It can then easily be imported into Excel or various 
>other standard problems (including R, for principal coordinate 
>analysis). If you need more information, I suggest you contact me 
>off the list.
>
>	Sincerely,
>
>	Michel
>
>>Hi,
>>Would anyone help me figure out how I can get a list of pairwise 
>>distances between taxa in Mesquite? It is simple to get the 
>>scattergram for all pairwise distances, or the underlying list of 
>>numbers, but I need the information for each pair of taxa. For 
>>example, I need a list with three columns, Taxon1, Taxon2, 
>>Distance. I am interested in simple patristic distances implied by 
>>the tree for morphological data, or molecular distances using a 
>>sequence matrix, a tree and a model. Is it possible in Mesquite?
>>Thanks in advance!
>>Jiri
>>
>>
>>
>>_______________________________________________
>>Mesquitelist mailing list
>>Mesquitelist at mesquiteproject.org
>>http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
>
>--
>Michel Laurin
>UMR CNRS 5143 "Centre de Recherches sur la Pal?obiodiversit? et les 
>Pal?oenvironnements"
>Mus?um National d'Histoire Naturelle
>D?partement Histoire de la Terre
>B?timent de G?ologie
>Case Postale 48
>57 rue Cuvier
>F-75231 PARIS Cedex 05
>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 dhearn at email.arizona.edu  Thu Jan 15 15:35:05 2009
From: dhearn at email.arizona.edu (dhearn at email.arizona.edu)
Date: Thu, 15 Jan 2009 16:35:05 -0700
Subject: [Mesquitelist] saving a legend as pdf?
Message-ID: <20090115163505.1b8pw408w4w0004o@www.email.arizona.edu>

Hello,

Relatively quick question... I've reconstructed the character histories of both
binary and continuous-valued traits. When I export the tree with the character
mapping as a pdf, the legend doesn't seem to be saved. Is there a way to save
the legend as a pdf?

Thanks,
David




From wmaddisn at interchange.ubc.ca  Thu Jan 15 21:31:40 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Thu, 15 Jan 2009 21:31:40 -0800
Subject: [Mesquitelist] saving a legend as pdf?
In-Reply-To: <20090115163505.1b8pw408w4w0004o@www.email.arizona.edu>
References: <20090115163505.1b8pw408w4w0004o@www.email.arizona.edu>
Message-ID: <a06240804c595cbacea4b@[192.168.0.188]>

At present the direct PDF saving doesn't save the trace character 
legend.  However, if you ask to print the tree instead, and then in 
the print dialog you print to a file, the postscript or pdf file 
saved should show the trace character legend.

In general it's a good idea to try both means of saving pdf's 
(direct, and through the Print dialog), to see which result suits you 
best.  They use different code.
Wayne


At 4:35 PM -0700 15.1.2009, dhearn at email.arizona.edu wrote:
>Hello,
>
>Relatively quick question... I've reconstructed the character 
>histories of both
>binary and continuous-valued traits. When I export the tree with the character
>mapping as a pdf, the legend doesn't seem to be saved. Is there a way to save
>the legend as a pdf?
>
>Thanks,
>David
>
>
>
>_______________________________________________
>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 patiny.s at gmail.com  Sat Jan 17 12:41:34 2009
From: patiny.s at gmail.com (=?ISO-8859-1?Q?S=E9bastien_Patiny?=)
Date: Sat, 17 Jan 2009 21:41:34 +0100
Subject: [Mesquitelist] dataset length
Message-ID: <686090a70901171241i434f08dct41e9acac65357732@mail.gmail.com>

Hi,

I am using Mesquite to manage a very large dataset multiple genes for some
hundreds taxa.  I doing individual genes  files, then no  problem with the
number of characters.  By contrast, I gonna have to pool several hundreds
taxa, is there a limit in the number of taxa included in a mesquite project?

Seb

-- 
----------------------------------------------------
Dr S?bastien Patiny
(Entomologist)
Chemcom s.a.
802 route de Lennik
1070 Brussels
BELGIUM
phone : + 32 (0)2 529.00.15
Fax    : + 32 (0)2 529.81.41
url : http://spatinyentomologist.blogspot.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090117/fa6bd7cf/attachment.html 

From wmaddisn at interchange.ubc.ca  Mon Jan 19 08:32:25 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Mon, 19 Jan 2009 08:32:25 -0800
Subject: [Mesquitelist] dataset length
In-Reply-To: <686090a70901171241i434f08dct41e9acac65357732@mail.gmail.com>
References: <686090a70901171241i434f08dct41e9acac65357732@mail.gmail.com>
Message-ID: <a06240802c59a5a037797@[192.168.0.188]>

At 9:41 PM +0100 17.1.2009, S?bastien Patiny wrote:
>Hi,
>
>I am using Mesquite to manage a very large dataset multiple genes 
>for some hundreds taxa.  I doing individual genes  files, then no 
>problem with the number of characters.  By contrast, I gonna have to 
>pool several hundreds taxa, is there a limit in the number of taxa 
>included in a mesquite project?

The limit is mostly determined by the memory available to you.  You 
should be able to handle a few thousand taxa without too much 
trouble.  Notice there are instructions in Mesquite_Folder on how to 
increase memory available to Mesquite.

If you need to give more than about 2GB to Mesquite, then you will 
need to use a 64 bit java virtual machine.  To do that, it may 
suffice (depending on your computer and operating system) to add -d64 
to the command line arguments in the shell script/batch script that 
you use to start Mesquite.

We are working on some speed issues with big matrices; we hope to 
have them resolved soon.

Wayne

>
>Seb
>
>--
>----------------------------------------------------
>Dr S?bastien Patiny
>(Entomologist)
>Chemcom s.a.
>802 route de Lennik
>1070 Brussels
>BELGIUM
>phone : + 32 (0)2 529.00.15
>Fax    : + 32 (0)2 529.81.41
>url : 
><http://spatinyentomologist.blogspot.com/>http://spatinyentomologist.blogspot.com/
>
>_______________________________________________
>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 mguerrini at biologia.unipi.it  Thu Jan 22 03:35:42 2009
From: mguerrini at biologia.unipi.it (Monica Guerrini)
Date: Thu, 22 Jan 2009 12:35:42 +0100
Subject: [Mesquitelist] S-values and correct gene tree
Message-ID: <20090122113504.C352EBBC575@mailserver.biologia.unipi.it>

Hello!
I start to use Mesquite few days ago. I'm trying to test a model of 
population history utilizing a set of 95 sequences. I estimate the 
divergence time and I should use these generation numbers. But I'm 
not sure to perform the correct simulations. I have reconstructed a 
population tree using the drawing option. Then I calculate the 
distribution of S-values and the percentiles (0.05). Now I should 
compare these values to the S-value of my gene tree (for both 
calculated using different numbers of Ne). But which gene tree? I try 
to perform a gene tree with Mesquite (the option of "new tree 
window")...... but I haven't understood if I should create a new tree 
using Mesquite or if I should use a gene tree obtained from different 
elaboration. Infact I performed NJ distance tree and Maximum 
Parsimony tree with PAUP. But if yes, how can I import the tree and 
open the drawing into the tree window?
Thank you very much.... I read the manual but I don't find the 
answers to my problems.... !!!

Bye bye

Monica


From d.a.henk at gmail.com  Thu Jan 22 06:50:45 2009
From: d.a.henk at gmail.com (Daniel)
Date: Thu, 22 Jan 2009 14:50:45 +0000
Subject: [Mesquitelist] S-values and correct gene tree
In-Reply-To: <20090122113504.C352EBBC575@mailserver.biologia.unipi.it>
References: <20090122113504.C352EBBC575@mailserver.biologia.unipi.it>
Message-ID: <4224e620901220650i426d25c7r6619a64bd1cc82c1@mail.gmail.com>

Hi Monica,

If I understand what you've done then you have sets of s-values from gene
trees generated in Mesquite under different models of population history.
The s-value to compare against the simulated s-values should probably come
from your best inferred genealogy (or set of probable genealogies) vs your
hypothetical population histories. You can get the s-value by opening your
inferred from MrBayes/PAUP/etc gene tree in Mesquite (include file -> choose
your tree file) and calculating the s-value vs each population tree (tree
window -> analysis -> values for current tree -> s of ...) . You could store
your simulated sets of trees as separate treeblocks and simply add your tree
inferred from PAUP/MrBayes/NJ/or whatever by storing it in those treeblocks.
Then you'll be able to see the s-value for that tree along with all the
simulated trees for each hypothesis in a histogram right in Mesquite, and
you could use the handy contained tree drawings to show your genealogy
inside the population tree, but I don't think Mesquite should be used to
infer a gene tree. I hope that makes sense.

Someone please correct me if I'm going astray here.

best,
daniel


2009/1/22 Monica Guerrini <mguerrini at biologia.unipi.it>

> Hello!
> I start to use Mesquite few days ago. I'm trying to test a model of
> population history utilizing a set of 95 sequences. I estimate the
> divergence time and I should use these generation numbers. But I'm
> not sure to perform the correct simulations. I have reconstructed a
> population tree using the drawing option. Then I calculate the
> distribution of S-values and the percentiles (0.05). Now I should
> compare these values to the S-value of my gene tree (for both
> calculated using different numbers of Ne). But which gene tree? I try
> to perform a gene tree with Mesquite (the option of "new tree
> window")...... but I haven't understood if I should create a new tree
> using Mesquite or if I should use a gene tree obtained from different
> elaboration. Infact I performed NJ distance tree and Maximum
> Parsimony tree with PAUP. But if yes, how can I import the tree and
> open the drawing into the tree window?
> Thank you very much.... I read the manual but I don't find the
> answers to my problems.... !!!
>
> Bye bye
>
> Monica
>
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/ae36c597/attachment.html 

From jeffrey.oliver at yale.edu  Thu Jan 22 07:47:19 2009
From: jeffrey.oliver at yale.edu (Jeffrey C. Oliver)
Date: Thu, 22 Jan 2009 10:47:19 -0500
Subject: [Mesquitelist] S-values and correct gene tree
In-Reply-To: <20090122113504.C352EBBC575@mailserver.biologia.unipi.it>
References: <20090122113504.C352EBBC575@mailserver.biologia.unipi.it>
Message-ID: <fcb0cd600901220747i6789926ex577c8b284b897dba@mail.gmail.com>

Hi Monica,

There is some information on this type of analysis in the Mesquite Manual
FAQ:

http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/MesquiteFAQ.html#sms

And a short guide which provides a worked example:

http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/slatkinMaddisonS.html

-Jeff

On Thu, Jan 22, 2009 at 6:35 AM, Monica Guerrini <
mguerrini at biologia.unipi.it> wrote:

> Hello!
> I start to use Mesquite few days ago. I'm trying to test a model of
> population history utilizing a set of 95 sequences. I estimate the
> divergence time and I should use these generation numbers. But I'm
> not sure to perform the correct simulations. I have reconstructed a
> population tree using the drawing option. Then I calculate the
> distribution of S-values and the percentiles (0.05). Now I should
> compare these values to the S-value of my gene tree (for both
> calculated using different numbers of Ne). But which gene tree? I try
> to perform a gene tree with Mesquite (the option of "new tree
> window")...... but I haven't understood if I should create a new tree
> using Mesquite or if I should use a gene tree obtained from different
> elaboration. Infact I performed NJ distance tree and Maximum
> Parsimony tree with PAUP. But if yes, how can I import the tree and
> open the drawing into the tree window?
> Thank you very much.... I read the manual but I don't find the
> answers to my problems.... !!!
>
> Bye bye
>
> Monica
>
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/de25ad45/attachment.html 

From rcgarrick at vcu.edu  Thu Jan 22 08:21:30 2009
From: rcgarrick at vcu.edu (Ryan C Garrick/FS/VCU)
Date: Thu, 22 Jan 2009 11:21:30 -0500
Subject: [Mesquitelist] S-values and correct gene tree
Message-ID: <OFEC35A97D.7C341B18-ON85257546.0059DB92-85257546.0059DBF4@vcu.edu>

An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/132b9498/attachment-0001.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Mesquite excercises.pdf
Type: application/pdf
Size: 457302 bytes
Desc: not available
Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/132b9498/attachment-0001.pdf 

From wmaddisn at interchange.ubc.ca  Sat Jan 24 16:38:29 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Sat, 24 Jan 2009 16:38:29 -0800
Subject: [Mesquitelist] Mesquite 2.6 released
Message-ID: <a06240802c5a1616854db@[192.168.0.157]>

Mesquite 2.6 has been released at http://mesquiteproject.org.  If you 
are running Mesquite 2.5, you should receive notice of this when you 
start Mesquite.

There are some important bug fixes, and all users are urged to 
upgrade.  You can see a full list of changes and important bug fixes 
at 
http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/changes.html.

Among the new features is an option to simplify the interface by 
hiding menu items and tools you might not be likely to use.  There 
are some built-in simplification themes (e.g., MacClade-like; 
population genetics; etc.), and you can build your own.  You might 
find this especially useful for teaching courses.


-- 
-------------------------------------------------------------------
Wayne Maddison                        David R. Maddison
Departments of Zoology and Botany     Department of Entomology
University of British Columbia        University of Arizona
Vancouver, BC   V6T 1Z4               Tucson, AZ   85721
email: wmaddisn at interchange.ubc.ca    email: beetle at ag.arizona.edu

Mesquite: http://mesquiteproject.org
MacClade: http://macclade.org
Tree of Life: http://tolweb.org

From mguerrini at biologia.unipi.it  Mon Jan 26 01:49:51 2009
From: mguerrini at biologia.unipi.it (Monica Guerrini)
Date: Mon, 26 Jan 2009 10:49:51 +0100
Subject: [Mesquitelist] S- value
In-Reply-To: <mailman.70.1232647697.99.mesquitelist@mesquiteproject.org>
References: <mailman.70.1232647697.99.mesquitelist@mesquiteproject.org>
Message-ID: <20090126094915.49D63BBC043@mailserver.biologia.unipi.it>

Hi!
Thank you very much for your answers! Now I have 
resolved my first problem, that is importing and 
using a gene tree reconstructed with other programs! It is very easy!!!!
But now I have another two questions.
First of all, if I measure the distributions of 
test statistics (Slatkin & Maddison's S) on a 
simulated population tree, when I reject or 
accept this model drawn? I know that if the 
observed S.-value of my gene tree falls outside 
of the 95% confidence interval, that model are 
not supported by the data. On the contrary, if I 
have a case similar to the example of Mesquite's 
manual I don't reject the model (S = 9, observed 
values within the 95% confidence interval, that is 4 and 10).
But now I suppose this example:
I measure the observed S-value for my first gene 
tree and that is 9 (for example...!).
Now I draw some population trees corresponding to 
the evolution models I want to test. I measure 
the distribution of S-values for each model.
model n? 1: the S-value distribution has only one 
value, for example 2, so I reject the model (outside the boundary)
model n?2: the S-value distribution has two 
limits: 5 and 15, so I accept the model (inside the boundary)
model n?3: the S-value distribution has only one 
value, that is 9 (exactly my observed S-value)      ??????
model n?4: the S-value distribution has two 
limits: 9 and 15 (lower tail exactly my observed S-value)      ??????
What happen for models n? 3 and 4? I'm not sure 
to accept or reject these hypothesis.......

The second question is:
For use a gene tree (reconstructed with other 
software) and to measure S-value it is better to 
use a sequences tree or an haplotypes tree?

Thank you very very much again for your help!!!!!


Monica











  At 19.08 22/01/2009, you wrote:
>Send Mesquitelist mailing list submissions to
>         mesquitelist at mesquiteproject.org
>
>To subscribe or unsubscribe via the World Wide Web, visit
>         http://mesquiteproject.org/mailman/listinfo/mesquitelist
>or, via email, send a message with subject or body 'help' to
>         mesquitelist-request at mesquiteproject.org
>
>You can reach the person managing the list at
>         mesquitelist-owner at mesquiteproject.org
>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Mesquitelist digest..."
>
>
>Today's Topics:
>
>    1. S-values and correct gene tree (Monica Guerrini)
>    2. Re: S-values and correct gene tree (Daniel)
>    3. Re: S-values and correct gene tree (Jeffrey C. Oliver)
>    4. S-values and correct gene tree (Ryan C Garrick/FS/VCU)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 22 Jan 2009 12:35:42 +0100
>From: Monica Guerrini <mguerrini at biologia.unipi.it>
>Subject: [Mesquitelist] S-values and correct gene tree
>To: mesquitelist at mesquiteproject.org
>Message-ID: <20090122113504.C352EBBC575 at mailserver.biologia.unipi.it>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>Hello!
>I start to use Mesquite few days ago. I'm trying to test a model of
>population history utilizing a set of 95 sequences. I estimate the
>divergence time and I should use these generation numbers. But I'm
>not sure to perform the correct simulations. I have reconstructed a
>population tree using the drawing option. Then I calculate the
>distribution of S-values and the percentiles (0.05). Now I should
>compare these values to the S-value of my gene tree (for both
>calculated using different numbers of Ne). But which gene tree? I try
>to perform a gene tree with Mesquite (the option of "new tree
>window")...... but I haven't understood if I should create a new tree
>using Mesquite or if I should use a gene tree obtained from different
>elaboration. Infact I performed NJ distance tree and Maximum
>Parsimony tree with PAUP. But if yes, how can I import the tree and
>open the drawing into the tree window?
>Thank you very much.... I read the manual but I don't find the
>answers to my problems.... !!!
>
>Bye bye
>
>Monica
>
>
>
>------------------------------
>
>Message: 2
>Date: Thu, 22 Jan 2009 14:50:45 +0000
>From: Daniel <d.a.henk at gmail.com>
>Subject: Re: [Mesquitelist] S-values and correct gene tree
>To: Monica Guerrini <mguerrini at biologia.unipi.it>
>Cc: mesquitelist at mesquiteproject.org
>Message-ID:
>         <4224e620901220650i426d25c7r6619a64bd1cc82c1 at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi Monica,
>
>If I understand what you've done then you have sets of s-values from gene
>trees generated in Mesquite under different models of population history.
>The s-value to compare against the simulated s-values should probably come
>from your best inferred genealogy (or set of probable genealogies) vs your
>hypothetical population histories. You can get the s-value by opening your
>inferred from MrBayes/PAUP/etc gene tree in Mesquite (include file -> choose
>your tree file) and calculating the s-value vs each population tree (tree
>window -> analysis -> values for current tree -> s of ...) . You could store
>your simulated sets of trees as separate treeblocks and simply add your tree
>inferred from PAUP/MrBayes/NJ/or whatever by storing it in those treeblocks.
>Then you'll be able to see the s-value for that tree along with all the
>simulated trees for each hypothesis in a histogram right in Mesquite, and
>you could use the handy contained tree drawings to show your genealogy
>inside the population tree, but I don't think Mesquite should be used to
>infer a gene tree. I hope that makes sense.
>
>Someone please correct me if I'm going astray here.
>
>best,
>daniel
>
>
>2009/1/22 Monica Guerrini <mguerrini at biologia.unipi.it>
>
> > Hello!
> > I start to use Mesquite few days ago. I'm trying to test a model of
> > population history utilizing a set of 95 sequences. I estimate the
> > divergence time and I should use these generation numbers. But I'm
> > not sure to perform the correct simulations. I have reconstructed a
> > population tree using the drawing option. Then I calculate the
> > distribution of S-values and the percentiles (0.05). Now I should
> > compare these values to the S-value of my gene tree (for both
> > calculated using different numbers of Ne). But which gene tree? I try
> > to perform a gene tree with Mesquite (the option of "new tree
> > window")...... but I haven't understood if I should create a new tree
> > using Mesquite or if I should use a gene tree obtained from different
> > elaboration. Infact I performed NJ distance tree and Maximum
> > Parsimony tree with PAUP. But if yes, how can I import the tree and
> > open the drawing into the tree window?
> > Thank you very much.... I read the manual but I don't find the
> > answers to my problems.... !!!
> >
> > Bye bye
> >
> > Monica
> >
> > _______________________________________________
> > Mesquitelist mailing list
> > Mesquitelist at mesquiteproject.org
> > http://mesquiteproject.org/mailman/listinfo/mesquitelist
> >
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: 
>http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/ae36c597/attachment-0001.html 
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 22 Jan 2009 10:47:19 -0500
>From: "Jeffrey C. Oliver" <jeffrey.oliver at yale.edu>
>Subject: Re: [Mesquitelist] S-values and correct gene tree
>To: Monica Guerrini <mguerrini at biologia.unipi.it>,
>         mesquitelist at mesquiteproject.org
>Message-ID:
>         <fcb0cd600901220747i6789926ex577c8b284b897dba at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi Monica,
>
>There is some information on this type of analysis in the Mesquite Manual
>FAQ:
>
>http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/MesquiteFAQ.html#sms
>
>And a short guide which provides a worked example:
>
>http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/Help/slatkinMaddisonS.html
>
>-Jeff
>
>On Thu, Jan 22, 2009 at 6:35 AM, Monica Guerrini <
>mguerrini at biologia.unipi.it> wrote:
>
> > Hello!
> > I start to use Mesquite few days ago. I'm trying to test a model of
> > population history utilizing a set of 95 sequences. I estimate the
> > divergence time and I should use these generation numbers. But I'm
> > not sure to perform the correct simulations. I have reconstructed a
> > population tree using the drawing option. Then I calculate the
> > distribution of S-values and the percentiles (0.05). Now I should
> > compare these values to the S-value of my gene tree (for both
> > calculated using different numbers of Ne). But which gene tree? I try
> > to perform a gene tree with Mesquite (the option of "new tree
> > window")...... but I haven't understood if I should create a new tree
> > using Mesquite or if I should use a gene tree obtained from different
> > elaboration. Infact I performed NJ distance tree and Maximum
> > Parsimony tree with PAUP. But if yes, how can I import the tree and
> > open the drawing into the tree window?
> > Thank you very much.... I read the manual but I don't find the
> > answers to my problems.... !!!
> >
> > Bye bye
> >
> > Monica
> >
> > _______________________________________________
> > Mesquitelist mailing list
> > Mesquitelist at mesquiteproject.org
> > http://mesquiteproject.org/mailman/listinfo/mesquitelist
> >
>-------------- next part --------------
>An HTML attachment was scrubbed...
>URL: 
>http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/de25ad45/attachment-0001.html 
>
>
>------------------------------
>
>Message: 4
>Date: Thu, 22 Jan 2009 11:21:30 -0500
>From: Ryan C Garrick/FS/VCU <rcgarrick at vcu.edu>
>Subject: [Mesquitelist] S-values and correct gene tree
>To: Monica at mesquiteproject.org, "Guerrini
>         <mguerrini"@biologia.unipi.it,  mesquitelist at mesquiteproject.org
>Message-ID:
>         <OFEC35A97D.7C341B18-ON85257546.0059DB92-85257546.0059DBF4 at vcu.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>An HTML attachment was scrubbed...
>URL: 
>http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/132b9498/attachment.html 
>
>-------------- next part --------------
>A non-text attachment was scrubbed...
>Name: Mesquite excercises.pdf
>Type: application/pdf
>Size: 457302 bytes
>Desc: not available
>Url : 
>http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090122/132b9498/attachment.pdf 
>
>
>------------------------------
>
>_______________________________________________
>Mesquitelist mailing list
>Mesquitelist at mesquiteproject.org
>http://mesquiteproject.org/mailman/listinfo/mesquitelist
>
>
>End of Mesquitelist Digest, Vol 33, Issue 8
>*******************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090126/94479948/attachment.html 

From kipwill at berkeley.edu  Thu Jan 29 13:55:58 2009
From: kipwill at berkeley.edu (Kipling (Kip) Will)
Date: Thu, 29 Jan 2009 13:55:58 -0800
Subject: [Mesquitelist] Problems with alignment
Message-ID: <498225EE.7060306@berkeley.edu>

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

-- 
Kipling W. Will
Associate Professor/Insect Systematist
Associate Director,Essig Museum of Entomology

mail to:
137 Mulford Hall
ESPM Dept.- Organisms & Environment Div.
University of California
Berkeley, California 94720

phone 510-642-4296
fax 510-643-5438


From wmaddisn at interchange.ubc.ca  Fri Jan 30 09:20:24 2009
From: wmaddisn at interchange.ubc.ca (Wayne Maddison)
Date: Fri, 30 Jan 2009 09:20:24 -0800
Subject: [Mesquitelist] Problems with alignment
In-Reply-To: <498225EE.7060306@berkeley.edu>
References: <498225EE.7060306@berkeley.edu>
Message-ID: <a0624081cc5a8e7011a2d@[137.82.80.142]>

Could you send to us off-list the log file produced during a run when 
this happens?
thanks,
Wayne


At 1:55 PM -0800 29.1.2009, Kipling (Kip) Will wrote:
>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
>
>--
>Kipling W. Will
>Associate Professor/Insect Systematist
>Associate Director,Essig Museum of Entomology
>
>mail to:
>137 Mulford Hall
>ESPM Dept.- Organisms & Environment Div.
>University of California
>Berkeley, California 94720
>
>phone 510-642-4296
>fax 510-643-5438
>
>_______________________________________________
>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 budd at embl-heidelberg.de  Sat Jan 31 13:37:16 2009
From: budd at embl-heidelberg.de (Aidan Budd)
Date: Sat, 31 Jan 2009 22:37:16 +0100 (CET)
Subject: [Mesquitelist] labeling duplication/extinctions on contained tree?
Message-ID: <Pine.LNX.4.44.0901312236590.16644-100000@bibo.EMBL-Heidelberg.DE>

Hi Mesquiters,

I've been using Mesquite to reconcile gene and species trees to estimate
minimum numbers of duplication/extinction events - and it's working great

I'm planning on using this for some teaching - to show how ANY gene tree 
can be reconciled with any species tree - and for this I've been looking 
for a way to highlight in the contained tree window the nodes that are are 
duplications, and ideally also to label the extinctions (I have trouble 
spotting them, so I guess the students will too!) 

Would be great if you could let me know whether or not it's possible to do 
something like this with Mesquite - maybe label the duplication nodes a 
particular colour? Show extinctions with a cross indicating loss of the 
lineage?

Any advice/suggestions happily received!

Thanks

Aidan

-- 
----------------------------------------------------------------------
Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
Meyerhofstr. 1, 69117 Heidelberg, Germany

http://www.embl-heidelberg.de/~budd/
http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html