From wmaddisn at interchange.ubc.ca Sun May 3 18:29:22 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 03 May 2009 18:29:22 -0700 Subject: [Mesquitelist] Mesquite cannot write log file In-Reply-To: <756114095.1734741239842133775.JavaMail.root@erie.cs.uoguelph.ca> References: <756114095.1734741239842133775.JavaMail.root@erie.cs.uoguelph.ca> Message-ID: Some of you are getting a message that Mesquite does not have permission to write its log file. This message is given in error. It is a simple bug we'll have fixed in the next version. The message is usually given if the Mesquite_Support_Files directory is present, but there is no Mesquite_Log file within it. The solution is to delete the Mesquite_Support_Files folder, and then start Mesquite again. Some preferences will be lost. If later you want to get a copy of the Mesquite_Log file, don't move it, but rather copy it out. Wayne -- -------------------------------------------------------- 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 May 3 18:29:43 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 03 May 2009 18:29:43 -0700 Subject: [Mesquitelist] Logging the results of analyses In-Reply-To: References: Message-ID: The most powerful way to do this is via scripting. In scripting you can obtain the results as text then save them to files. Give the command getLastResultString or getLastResult to the module, and then put the returned string into a text file. I'll attach an example script. If you want the results for a whole series of trees, visible in the tree window, then you can go to the tree window, set up the calculation in the tree window as desired, then choose Step Through Trees in the Tree window. You can also save results from charts, including parameter values estimated in some cases. Do any of these do what you want? Wayne At 12:48 PM +0200 24.4.2009, Aidan Budd wrote: >Hi Alejandro > >Thanks for writing back so quickly > >In fact, that's not what I'm trying to do - rather, I have a set of >phylogenies which describe relatioships between different sets of taxa >(they are trees esimated from several different gene families) > >I'm looking, then, for trends in the evolutionary dynamics of features of >the proteins, and (amongst other things) would be interested to see >whether there are common trends in different types of characters across >the different families > >While I'll want to look through the results of each family "manually", I'd >also like to write the results in a way that doesn't involve >copying-and-pasting the likelihoods and rate parameter values for each >analysis into a spreadsheet, to make overal trends easier to spot - hence >looking for a way to get the results of these analyses printed out from >MESQUTE > >Perhaps I should just use Pagel's software directly, or use PAUP*, or >something else, if I'm looking to generate those kinds of summaries >(although i'd stick with using MESQUITE for the browsing of the data - >just seems a shame to repeat the same thing in different software liket >that...) > >Thanks again > >Aidan > > >On Fri, 24 Apr 2009, Alejandro Gonzalez Voyer wrote: > >> Hello Aidan, >> >> I've missed previous posts so I'm not 100% certain if I understood your >> question correctly. If what you want to do is compare an independent versus >> a dependent model of evolution for two binary traits across a subsample of >> likely phylogenies (taking phylogenetic uncertainty into account) then you >> should instead use Bayestraits. In Bayestraits you can also compare rates of >> "gains" versus "losses" of the two traits etc. >> You could have a look at: Pagel and Meade 2006 Bayesian analysis of >> correlated evolution of discrete characters by Reversible-Jump Markov Chain >> Monte Carlo. Am Nat 167: 808-825. >> >> Cheers, >> >> Alejandro >> >> -----Original Message----- >> From: mesquitelist-bounces at mesquiteproject.org >> [mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of Aidan Budd >> Sent: den 24 april 2009 12:29 >> To: mesquitelist at mesquiteproject.org >> Subject: [Mesquitelist] Logging the results of analyses >> >> hi again, MESQUITEers >> >> I'm looking for a way to have MESQUITE write the **results** of its >> analyses to a text file >> >> Thanks to Daniel, I can now do the ML analysis of binary characters I was >> looking for in MESQUITE (comparing Mk1 and AsymmMk1 with LRTs). >> >> I'm doing this for 100 or so different tree/character datasets, and would >> like to keep a text record of the results of each analysis i.e. the >> likelihoods under the two different models, the results of correlation >> analyses etc. - I'll be browsing through each analysis using MESQUITE's >> GUI, but I'd also like to store information in a file to look at in a >> spreadsheet etc. (e.g. to compare the forward/backward rates of all ML >> AsymmMk1 models from all trees and characters - is forward always faster >> than backward? - questions like that) >> >> The MESQUITE log records the commands I issue, but I was hoping to find >> also a facility that logs also/only the **results** of analyses of this >> kind. >> >> I know I can look at the text representation of the trees, but this only > > describes the results of the most-recently done analysis (e.g. if I first >> check for correlation between characters 1 and 2, and then between >> characters 2 and 3, this window will only describe the log likelihood >> difference between chars 2 and 3) - I'd like to record the results of >> **all** these analyses. >> >> Any pointers to how to convince MESQUITE to do something like this much >> appreciated! >> >> Or perhaps this is simply something that MESQUITE isn't designed to be >> able to do and I should be trying out alternative software...? >> >> 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 > >_______________________________________________ >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 -------------- next part -------------- A non-text attachment was scrubbed... Name: assessorSEqual.txt Type: application/octet-stream Size: 2379 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090503/a4cc93fb/attachment.obj From wmaddisn at interchange.ubc.ca Sun May 3 18:29:54 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 03 May 2009 18:29:54 -0700 Subject: [Mesquitelist] running MESQUITE from the command line - specifying a project file to open In-Reply-To: References: Message-ID: Open up Run_Mesquite_OSX.command in a text editor; you'll see a line like java -Xmx500M -Xss2m -Djava.library.path=lib -cp "$dir" mesquite.Mesquite Basically, you'll enter something like that in Terminal. First, find the path to Mesquite_Folder. Suppose it's in /Applications. Second, find the path to your data file. Suppose it's on your user Desktop, i.e. "/Users/Budd/Desktop/myMesquiteNexusProject.nxs" Now open Terminal. Enter the command: java -Xmx500M -Xss2m -Djava.library.path=lib -cp /Applications/Mesquite_Folder mesquite.Mesquite '/Users/Budd/Desktop/myMesquiteNexusProject.nxs' Alternatively, open up Mesquite without a file, then, from the command line, request a file to be opened: openfile '/Users/Budd/Desktop/myMesquiteNexusProject.nxs' If you don't want the windows to appear, include -w in the arguments: java -Xmx500M -Xss2m -Djava.library.path=lib -cp /Applications/Mesquite_Folder mesquite.Mesquite '/Users/Budd/Desktop/myMesquiteNexusProject.nxs' -w You could also use the headless version. A hint: when operating Mesquite by the command line, you can find the list of high level commands by typing "help". Even in the headless version there is a sense of "windows" existing, which you can find and command using sw and jw. You can find the list of commands specific to the object being commanded by typing ?. Wayne At 10:25 AM +0200 29.4.2009, Aidan Budd wrote: >Hi again, MESQUITEers > >Rather than tacking this on the end of my previous mail, thought it might >be better to give it a separate thread... > >I'd like to be able, on my OSX machine, to run/execute MESQUITE from the >command line in a way that specifies, via the command-line invocation, a >NEXUS file to open in MESQUITE. > >I can start MESQUITE no problem from the command line, simply invoking the >Run_Mesquite_OSX.command script > >However, knowing almost exactly nothing about java, I haven't been able to >work out how to alter the java invocation to specify a MESQUITE >NEXUS-format file to open on starting MESQUITE so that I can do something >like: > >Run_Mesquite_OSX.command myMesquiteNexusProject.nxs > >so that MESQUITE will start, and then open "myMesquiteNexusProject.nxs" > >Any suggestions on how to do this would be much appreciated - or, of >course, the advice to stop trying to do it as it's not appropriate/doesn't >make sense! > >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 > >_______________________________________________ >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 May 3 18:29:59 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 03 May 2009 18:29:59 -0700 Subject: [Mesquitelist] MESQUITE scripting - opening character and tree files In-Reply-To: References: Message-ID: Let me see if I understand what you want. You would like to open a file with matrix, then open a file with a tree, do a calculation, save the results to a file, then close both files, go on to the next matrix and tree, and so on? Is the calculation done dependent on a tree window or not? What exact calculation do you want done? There is no problem reading a series of files via a script, but exactly how this should be done will depend on just what calculation you want. Wayne At 10:19 AM +0200 29.4.2009, Aidan Budd wrote: >Hi MESQUITEers > >I'm trying to write MESQUITE scripts that will load trees stored in around >100 different PHYLIP/NEWICK-format tree files, and binary character data >(simple format) stored in the same number of external files (each of >the 100+ trees is associated with one of the binary character >datasets) such the appropriate tree/character-matrix pairs share the same >taxa blocks > >The "trick" of doing the analysis via the MESQUITE GUI, and then looking >at the MESQUITE scripting commands used to do the analysis doesn't work >here - completely appropriately, MESQUITE simply writes appropriate taxa, >tree, and charcter matrix NEXUS blocks based on the imported data, rather >than specifying the script commands needed to reach this state. > >I'd greatly appreciate if someone could post an example script that would >enable me to do something like this - I haven't been able to find an >example to help me with this. > >Alternatively, perhaps this is just not feasible using MESQUITE, and I >should rather put together a perl/python script that "simply" creates a >NEXUS format file with appropriate tree/taxa/character-matrix blocks...? > >(Somehow it'd be a shame, though, if this were the way to do it - I'd >rather avoid getting all the formating of these blocks right, parsing the >input files etc.) > >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 > > > >_______________________________________________ >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 jon.brate at bio.uio.no Mon May 11 03:55:06 2009 From: jon.brate at bio.uio.no (=?ISO-8859-1?Q?Jon_Br=E5te?=) Date: Mon, 11 May 2009 12:55:06 +0200 Subject: [Mesquitelist] Problem converting U's to T's Message-ID: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> Hi, we were aligning some 18S sequences and suddenly we realized that all the T's had changed to U's. We didn't notice when or how it happened and now we cannot find a way to convert them back to T's. Can anyone help us with this problem? Thank you in advance, Jon Br?te ------------------------------------------------------------- Jon Br?te PhD student Microbial Evolution Research Group (MERG) Department of Biology University of Oslo P.b. 1066 Blindern N-0316 Oslo Norway Phone: +47 22855083 From wmaddisn at interchange.ubc.ca Mon May 11 08:19:17 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 11 May 2009 08:19:17 -0700 Subject: [Mesquitelist] Problem converting U's to T's In-Reply-To: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> References: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> Message-ID: How were you doing the alignments -- with Opal, by hand, or by other means? Might you be able to send us a copy of the file before the conversion to U's, and a scond copy after the conversion to U's? If you can, send it directly to me and not to the Mesquite List. Wayne At 12:55 PM +0200 11.5.2009, Jon Br?te wrote: >Hi, > >we were aligning some 18S sequences and suddenly we realized that all >the T's had changed to U's. We didn't notice when or how it happened >and now we cannot find a way to convert them back to T's. Can anyone >help us with this problem? > >Thank you in advance, > >Jon Br?te > >------------------------------------------------------------- >Jon Br?te >PhD student > >Microbial Evolution Research Group (MERG) >Department of Biology >University of Oslo >P.b. 1066 Blindern >N-0316 Oslo >Norway >Phone: +47 22855083 > >_______________________________________________ >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 jon.brate at bio.uio.no Mon May 11 11:20:16 2009 From: jon.brate at bio.uio.no (jon.brate at bio.uio.no) Date: Mon, 11 May 2009 20:20:16 +0200 (CEST) Subject: [Mesquitelist] Problem converting U's to T's In-Reply-To: References: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> Message-ID: <296453775679f2d9790565760860f8bc.squirrel@webmail.uio.no> Hi, right now we fixed it. We changed the text in the nexus file, i.e. datatype=DNA. It was an imported alignment which we edited by hand. I guess we hit the convert DNA to RNA button and could not convert back. Thank you for the prompt reply, Jon > How were you doing the alignments -- with Opal, by hand, or by other > means? > > Might you be able to send us a copy of the file before the conversion > to U's, and a scond copy after the conversion to U's? If you can, > send it directly to me and not to the Mesquite List. > Wayne > > At 12:55 PM +0200 11.5.2009, Jon Br?te wrote: >>Hi, >> >>we were aligning some 18S sequences and suddenly we realized that all >>the T's had changed to U's. We didn't notice when or how it happened >>and now we cannot find a way to convert them back to T's. Can anyone >>help us with this problem? >> >>Thank you in advance, >> >>Jon Br?te >> >>------------------------------------------------------------- >>Jon Br?te >>PhD student >> >>Microbial Evolution Research Group (MERG) >>Department of Biology >>University of Oslo >>P.b. 1066 Blindern >>N-0316 Oslo >>Norway >>Phone: +47 22855083 >> >>_______________________________________________ >>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 KHayden at bennington.edu Mon May 11 14:18:11 2009 From: KHayden at bennington.edu (Hayden, Katherine M.) Date: Mon, 11 May 2009 17:18:11 -0400 Subject: [Mesquitelist] GSoC coder problems getting started References: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> Message-ID: <36DB60B1B53C764F9041382C4BCD67030162C9B0@ex01.bennington.edu> Hello list, I'm a GSoC coder for Mesquite and have yet to properly introduce myself on this list- I'll get to that soon. But before that I could use some help: I've gotten the Mesquite source code for the latest official release (from repository/mesquite/releases/current/) into Eclipse and created a Mesquite launch configuration, but Mesquite won't fully load. When I run it, it gets through loading the modules, but then spits out errors and stalls: ... 686 modules installed. (.:4061): Gtk-CRITICAL **: gtk_text_buffer_emit_insert: assertion `g_utf8_validate (text, len, NULL)' failed ... java.lang.InternalError: Gtk: gtk_text_buffer_emit_insert: assertion `g_utf8_validate (text, len, NULL)' failed at java.lang.reflect.Constructor.newInstance(libgcj.so.90) Haven't been able to find out anything specific or useful when googling any parts of the error and am not familiar enough with Mesquite to track the error back to line 4061 (if I'm interpreting that correctly). Could I have some help as to where to take this? I'm running Ubuntu 9.04 Jaunty, Eclipse 3.2.2. Kasia Katherine "Kasia" Hayden Bennington College, Class of 2011 312.576.8175 khayden at bennington.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090511/9fb12188/attachment.html From wmaddisn at interchange.ubc.ca Mon May 11 14:46:49 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 11 May 2009 14:46:49 -0700 Subject: [Mesquitelist] GSoC coder problems getting started In-Reply-To: <36DB60B1B53C764F9041382C4BCD67030162C9B0@ex01.bennington.edu> References: <359D78C2-A0A5-428F-8F23-77BE9375FFFC@bio.uio.no> <36DB60B1B53C764F9041382C4BCD67030162C9B0@ex01.bennington.edu> Message-ID: I've never seen an error report like that, and I suspect there is a bug in your Java/Ubuntu. First, what version of Java are you using? Second, could you send to me off-list the log file (Mesquite_Log in Mesquite_Support_Files)? That's key in any error report. By the way, this mailing list is directed to users. There's a separate mailing list for Mesquite developers; see http://mesquiteproject.org/mesquite/development/development.html Wayne At 5:18 PM -0400 11.5.2009, Hayden, Katherine M. wrote: >Content-type: multipart/alternative; > boundary="Boundary_(ID_59lAUwv320P8rn2OlpNGMQ)" >Content-class: urn:content-classes:message > >Hello list, > >I'm a GSoC coder for Mesquite and have yet to properly introduce >myself on this list- I'll get to that soon. But before that I could >use some help: > >I've gotten the Mesquite source code for the latest official release >(from repository/mesquite/releases/current/) into Eclipse and >created a Mesquite launch configuration, but Mesquite won't fully >load. > >When I run it, it gets through loading the modules, but then spits >out errors and stalls: > >... >686 modules installed. >(.:4061): Gtk-CRITICAL **: gtk_text_buffer_emit_insert: assertion >`g_utf8_validate (text, len, NULL)' failed >... >java.lang.InternalError: Gtk: gtk_text_buffer_emit_insert: assertion >`g_utf8_validate (text, len, NULL)' failed > at java.lang.reflect.Constructor.newInstance(libgcj.so.90) > > > >Haven't been able to find out anything specific or useful when >googling any parts of the error and am not familiar enough with >Mesquite to track the error back to line 4061 (if I'm interpreting >that correctly). > >Could I have some help as to where to take this? I'm running Ubuntu >9.04 Jaunty, Eclipse 3.2.2. > > >Kasia > > > >Katherine "Kasia" Hayden >Bennington College, Class of 2011 >312.576.8175 >khayden at bennington.edu > > >_______________________________________________ >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 michelegreenfield at yahoo.com.au Thu May 14 00:34:59 2009 From: michelegreenfield at yahoo.com.au (Michele Greenfield) Date: Thu, 14 May 2009 00:34:59 -0700 (PDT) Subject: [Mesquitelist] Plotting characters onto a tree Message-ID: <543728.55408.qm@web33804.mail.mud.yahoo.com> Dear List, I would like to be able to add character labels onto a tree in Mesquite but cannot seem to find this functionality anywhere?? I believe this is something you could do in MacClade...or is it there and I have simply overlooked it? And if it is not there will it be implemented in any new versions? Thanking you Michele Greenfield Need a Holiday? Win a $10,000 Holiday of your choice. Enter now.http://us.lrd.yahoo.com/_ylc=X3oDMTJxN2x2ZmNpBF9zAzIwMjM2MTY2MTMEdG1fZG1lY2gDVGV4dCBMaW5rBHRtX2xuawNVMTEwMzk3NwR0bV9uZXQDWWFob28hBHRtX3BvcwN0YWdsaW5lBHRtX3BwdHkDYXVueg--/SIG=14600t3ni/**http%3A//au.rd.yahoo.com/mail/tagline/creativeholidays/*http%3A//au.docs.yahoo.com/homepageset/%3Fp1=other%26p2=au%26p3=mailtagline -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090514/f07de1d4/attachment.html From jon.brate at bio.uio.no Thu May 14 06:41:11 2009 From: jon.brate at bio.uio.no (=?ISO-8859-1?Q?Jon_Br=E5te?=) Date: Thu, 14 May 2009 15:41:11 +0200 Subject: [Mesquitelist] Calculating sum of branch lengths for clades Message-ID: <9E1F2EAB-E2EA-46B8-A6D7-D30AED0E2C34@bio.uio.no> Dear all, I am trying to calculate total branch lengths within different clades in a tree. Preferably also accounting for the number of taxa in each clade. I installed the Tuatara package for Mesquite in order to try the "Total Phylogenetic Diversity" option, but I cannot find or use this option. Can anybody help me with this? Thank you, Jon ------------------------------------------------------------- Jon Br?te PhD student Microbial Evolution Research Group (MERG) Department of Biology University of Oslo P.b. 1066 Blindern N-0316 Oslo Norway Phone: +47 22855083 From michel.laurin at upmc.fr Thu May 14 07:33:30 2009 From: michel.laurin at upmc.fr (Michel Laurin) Date: Thu, 14 May 2009 16:33:30 +0200 Subject: [Mesquitelist] Calculating sum of branch lengths for clades In-Reply-To: <9E1F2EAB-E2EA-46B8-A6D7-D30AED0E2C34@bio.uio.no> References: <9E1F2EAB-E2EA-46B8-A6D7-D30AED0E2C34@bio.uio.no> Message-ID: Dear Jon, My Stratigraphic Tools and StratAdds compute clade phylogenetic diversity (total path length in the clade), and can export phylogenetic distance matrices between all pairs of taxa, so if you install these (see the Mesquite home page), you should be all set. In addition, Mesquite itself can now export phylogenetic distance matrices (but not phylogenetic diversity, I think). Best wishes, Michel >Dear all, > >I am trying to calculate total branch lengths within different clades >in a tree. Preferably also accounting for the number of taxa in each >clade. I installed the Tuatara package for Mesquite in order to try >the "Total Phylogenetic Diversity" option, but I cannot find or use >this option. >Can anybody help me with this? > >Thank you, > >Jon > >------------------------------------------------------------- >Jon Br?te >PhD student > >Microbial Evolution Research Group (MERG) >Department of Biology >University of Oslo >P.b. 1066 Blindern >N-0316 Oslo >Norway >Phone: +47 22855083 > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- Michel Laurin UMR CNRS 7207 "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 43 rue Buffon F-75231 PARIS Cedex 05 FRANCE tel. (33 1) 40 79 34 68 http://tolweb.org/notes/?note_id=3669 From jgrant at smith.edu Mon May 18 10:28:33 2009 From: jgrant at smith.edu (Jessica Grant) Date: Mon, 18 May 2009 13:28:33 -0400 Subject: [Mesquitelist] is it possible to print trees over multiple pages? Message-ID: Hello, I was wondering if someone could help me with this. I am building large trees and would like to be able to print them over several pages. I have tried changing the tree size and then printing, but it has been hard to get it to print , for example, three pages high but only one page wide. Thank you! Jessica From victor_dill at hotmail.com Mon May 18 16:10:32 2009 From: victor_dill at hotmail.com (Victor Dill) Date: Mon, 18 May 2009 20:10:32 -0300 Subject: [Mesquitelist] reordering character states Message-ID: Hello all. I am constructing a morphological matrix. When adding mora taxa to the matrix, I realized that I needed to insert another, intermediate, state between two states of on given ordered character. In nexus, I would insert it as the last state and then reorder them. Is there a way to do this in Mesquite? Thanx all! Victor ----- Victor Goyannes Dill Orrico Doctoral student in Biological Sciences (Zoology) Online curriculum (http://lattes.cnpq.br/8248113511185358) Professional Address: UNESP - Universidade Estadual Paulista J?lio de Mesquita Filho Av. 24-A, num 744, Bela Vista, Departamento de Zoologia, I.B.; Cx. P. 199 CEP: 13506-900 - Rio Claro, SP - Brasil _________________________________________________________________ Conhe?a os novos produtos Windows Live! Clique aqui. http://www.windowslive.com.br -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090518/e101cb2a/attachment.html From wmaddisn at interchange.ubc.ca Sat May 23 21:03:02 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sat, 23 May 2009 21:03:02 -0700 Subject: [Mesquitelist] Plotting characters onto a tree In-Reply-To: <543728.55408.qm@web33804.mail.mud.yahoo.com> References: <543728.55408.qm@web33804.mail.mud.yahoo.com> Message-ID: An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090523/5247f88e/attachment.html From wmaddisn at interchange.ubc.ca Sat May 23 21:03:02 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sat, 23 May 2009 21:03:02 -0700 Subject: [Mesquitelist] Calculating sum of branch lengths for clades In-Reply-To: <9E1F2EAB-E2EA-46B8-A6D7-D30AED0E2C34@bio.uio.no> References: <9E1F2EAB-E2EA-46B8-A6D7-D30AED0E2C34@bio.uio.no> Message-ID: Michel's already answered regarding the availability of this function through his stratigraphic packages, but to clarify Tuatara's calculations: Total phylogenetic diversity is simply the sum of branch lengths over the whole tree; it doesn't partition it clade by clade. Otherwise the Tuatara package focuses on calculating values that pertain to terminal taxa, not to clades (e.g., conservation priority of a species). Wayne At 3:41 PM +0200 14.5.2009, Jon Br?te wrote: >Dear all, > >I am trying to calculate total branch lengths within different clades >in a tree. Preferably also accounting for the number of taxa in each >clade. I installed the Tuatara package for Mesquite in order to try >the "Total Phylogenetic Diversity" option, but I cannot find or use >this option. >Can anybody help me with this? > >Thank you, > >Jon > >------------------------------------------------------------- >Jon Br?te >PhD student > >Microbial Evolution Research Group (MERG) >Department of Biology >University of Oslo >P.b. 1066 Blindern >N-0316 Oslo >Norway >Phone: +47 22855083 > >_______________________________________________ >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 Sat May 23 21:03:02 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sat, 23 May 2009 21:03:02 -0700 Subject: [Mesquitelist] is it possible to print trees over multiple pages? In-Reply-To: References: Message-ID: There isn't a way to do this in Mesquite easily; you basically have to experiment with fixed drawing sizes (Tree window, Drawing>Drawing Size>Fixed Drawing size...) and printing using Print Tree... until you get what you need. It might be easier to save/print to a pdf, then find a program that can print PDF's over multiple pages. Wayne At 1:28 PM -0400 18.5.2009, Jessica Grant wrote: >Hello, > >I was wondering if someone could help me with this. I am building >large trees and would like to be able to print them over several >pages. I have tried changing the tree size and then printing, but it >has been hard to get it to print , for example, three pages high but >only one page wide. > >Thank you! > >Jessica >_______________________________________________ >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 Sat May 23 21:03:02 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sat, 23 May 2009 21:03:02 -0700 Subject: [Mesquitelist] reordering character states In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090523/3ea8154c/attachment.html From josephwb at umich.edu Sun May 24 05:36:07 2009 From: josephwb at umich.edu (Joseph Warren Brown) Date: Sun, 24 May 2009 08:36:07 -0400 Subject: [Mesquitelist] Tree sample manipulation Message-ID: <20090524083607.21641is58fq3s11c@web.mail.umich.edu> Y'All, I have a tree sample log file (from MrBayes) containing X trees for N taxa. I want to remove Y taxa (e.g. outgroup) from each tree and re-save the log file (i.e. X trees with N-Y taxa). I can successfully load the trees and the character matrix in Mesquite, as well as define the relevant taxon groups. However, when I try to delete the taxa they are only remove from the character matrix. Suggestions are appreciated. Thanks. Joseph. ______________________________________________________________ Joseph W. Brown, PhD Candidate Museum of Zoology, Bird Division 3015 Ruthven Museums Building 1109 Geddes Avenue University of Michigan, Ann Arbor MI 48109-1079 Fax: (734) 763-4080 Email: josephwb at umich.edu Homepage: http://www.umich.edu/~josephwb/ Family page: http://goghbirth.blogspot.com/ Calliope's page: http://calliopessnapshots.blogspot.com/ From wmaddisn at interchange.ubc.ca Mon May 25 08:52:50 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 25 May 2009 08:52:50 -0700 Subject: [Mesquitelist] Tree sample manipulation In-Reply-To: <20090524083607.21641is58fq3s11c@web.mail.umich.edu> References: <20090524083607.21641is58fq3s11c@web.mail.umich.edu> Message-ID: Mesquite has two ways to read tree files. (1) Using Include or Link file, or Import File With Trees, Mesquite reads in all the trees into memory at once. When Mesquite does this, and you delete taxa, the trees can be resaved with these taxa deleted. (2) Using Use Trees from Separate Nexus File, or Sample Trees from Separate Nexus File, or MrBayes Trees from .t File, Mesquite reads in the trees only one at a time, and leaves the remaining trees on disk, not in memory. In this second mode, the external tree file is treated as "read-only". If you delete taxa in the matrix, Mesquite doesn't go through the external tree file and delete those taxa from all the trees. I assume you read the trees from MrBayes using the second mode? You could read in the file using the first mode, but perhaps there are too many trees to hold in memory all at once. We will look into the possibility of simple transforming module that takes trees from one tree file, transforms them, and writes them straight into another file. This would be a useful module. Wayne At 8:36 AM -0400 24.5.2009, Joseph Warren Brown wrote: >Y'All, > >I have a tree sample log file (from MrBayes) containing X trees for N >taxa. I want to remove Y taxa (e.g. outgroup) from each tree and >re-save the log file (i.e. X trees with N-Y taxa). I can successfully >load the trees and the character matrix in Mesquite, as well as define >the relevant taxon groups. However, when I try to delete the taxa they >are only remove from the character matrix. > >Suggestions are appreciated. > >Thanks. >Joseph. >______________________________________________________________ >Joseph W. Brown, PhD Candidate >Museum of Zoology, Bird Division >3015 Ruthven Museums Building >1109 Geddes Avenue >University of Michigan, Ann Arbor MI 48109-1079 >Fax: (734) 763-4080 >Email: josephwb at umich.edu >Homepage: http://www.umich.edu/~josephwb/ >Family page: http://goghbirth.blogspot.com/ >Calliope's page: http://calliopessnapshots.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 josephwb at umich.edu Tue May 26 09:22:14 2009 From: josephwb at umich.edu (Joseph W. Brown) Date: Tue, 26 May 2009 12:22:14 -0400 Subject: [Mesquitelist] Tree sample manipulation In-Reply-To: References: <20090524083607.21641is58fq3s11c@web.mail.umich.edu> Message-ID: <207368B1-11F7-4885-916D-4B92BBE6A461@umich.edu> I was using the 'Include' approach, but my problem was that my tree log file contained both a Taxa block and a Translate block - deleting taxa from one block left my trees unaltered, but deleting them from the other block pruned the taxa from the trees as I had hoped. Thanks for the assistance. Joseph. On 25 May., 2009, at 11:52 , Wayne Maddison wrote: > Mesquite has two ways to read tree files. (1) Using Include or Link > file, or Import File With Trees, Mesquite reads in all the trees > into memory at once. When Mesquite does this, and you delete taxa, > the trees can be resaved with these taxa deleted. (2) Using Use > Trees from Separate Nexus File, or Sample Trees from Separate Nexus > File, or MrBayes Trees from .t File, Mesquite reads in the trees > only one at a time, and leaves the remaining trees on disk, not in > memory. In this second mode, the external tree file is treated as > "read-only". If you delete taxa in the matrix, Mesquite doesn't go > through the external tree file and delete those taxa from all the > trees. > > I assume you read the trees from MrBayes using the second mode? > > You could read in the file using the first mode, but perhaps there > are too many trees to hold in memory all at once. > > We will look into the possibility of simple transforming module that > takes trees from one tree file, transforms them, and writes them > straight into another file. This would be a useful module. > > Wayne > > > At 8:36 AM -0400 24.5.2009, Joseph Warren Brown wrote: >> Y'All, >> >> I have a tree sample log file (from MrBayes) containing X trees for >> N taxa. I want to remove Y taxa (e.g. outgroup) from each tree and >> re-save the log file (i.e. X trees with N-Y taxa). I can >> successfully load the trees and the character matrix in Mesquite, >> as well as define the relevant taxon groups. However, when I try to >> delete the taxa they are only remove from the character matrix. >> >> Suggestions are appreciated. >> >> Thanks. >> Joseph. >> ______________________________________________________________ >> Joseph W. Brown, PhD Candidate >> Museum of Zoology, Bird Division >> 3015 Ruthven Museums Building >> 1109 Geddes Avenue >> University of Michigan, Ann Arbor MI 48109-1079 >> Fax: (734) 763-4080 >> Email: josephwb at umich.edu >> Homepage: http://www.umich.edu/~josephwb/ >> Family page: http://goghbirth.blogspot.com/ >> Calliope's page: http://calliopessnapshots.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 > > ______________________________________________________________________________________________ Joseph W. Brown, PhD Candidate Museum of Zoology, Bird Division 3015 Ruthven Museums Building 1109 Geddes Avenue University of Michigan, Ann Arbor MI 48109-1079 Fax: (734) 763-4080 Email: josephwb at umich.edu Homepage: http://www.umich.edu/~josephwb/ Biology 162 Laboratory: http://www-personal.umich.edu/~josephwb/Biol162/Lab.html Tree of Life Web Project (Neornithes): http://tolweb.org/tree?group=Neornithes&contgroup=Aves Family page: http://goghbirth.blogspot.com/ Calliope's page: http://calliopessnapshots.blogspot.com/