From kari.allen at duke.edu Wed Mar 3 16:58:36 2010 From: kari.allen at duke.edu (Kari Allen) Date: Wed, 3 Mar 2010 19:58:36 -0500 Subject: [Mesquitelist] Independent Contrasts Questions Message-ID: <8c164dba1003031658y139b6673x1e4e5686909d455c@mail.gmail.com> Hi, I have two questions that I wondered if someone might be able to help me with. Transforming variables: Should you log your variables prior to the creation of independent contrasts? Or log the standardized contrasts after they are generated? I ask because subtraction in log space in effect becomes division, so I wonder what this does to the contrasts. Also: I am conducting a project in which one component has a strong allometric component (bodysize explains 94% of variance). I am trying to generate a LSR of this variable(y) on a second factor (x) to check for correlation. If I calculate residuals (nonphylogenetically, from tip data) for the y component, create contrasts for those residuals and for the raw x variable, standardized these contrasts and then regress y on x, I get a significant correlation (p=0.48, significant, but not impressive). If instead I generate contrasts for each variable-x, bodysize, and y-and then run a multiple regression (with bodymass on the x axis), I find no additive component from the target x variable. Is there a reason to prefer one method over the other? Hope this wasn't too confusing. Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100303/0a5133b0/attachment.html From tgarland at ucr.edu Wed Mar 3 17:03:57 2010 From: tgarland at ucr.edu (tgarland at ucr.edu) Date: Wed, 3 Mar 2010 17:03:57 -0800 (PST) Subject: [Mesquitelist] Independent Contrasts Questions In-Reply-To: <8c164dba1003031658y139b6673x1e4e5686909d455c@mail.gmail.com> References: <8c164dba1003031658y139b6673x1e4e5686909d455c@mail.gmail.com> Message-ID: <20100303170357.ARZ19022@fmh.ucr.edu> You must log traits BEFORE computing contrasts. Contrasts are just an algorithm, so don't worry about the apparent strangeness. I am a little confused by the second part of your question. You need to compute contrasts, then compute residuals, then correlate residuals. 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. 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 Garland, T., Jr., and M. R. Rose, eds. 2009. Experimental evolution: concepts, methods, and applications of selection experiments. University of California Press, Berkeley, California. http://www.ucpress.edu/books/pages/10604.php Associate Director Network for Experimental Research on Evolution http://nere.bio.uci.edu/ (A University of California Multicampus Research Project) ---- Original message ---- Date: Wed, 3 Mar 2010 19:58:36 -0500 From: Kari Allen Subject: [Mesquitelist] Independent Contrasts Questions To: mesquitelist at mesquiteproject.org Hi, I have two questions that I wondered if someone might be able to help me with. Transforming variables: Should you log your variables prior to the creation of independent contrasts? Or log the standardized contrasts after they are generated? I ask because subtraction in log space in effect becomes division, so I wonder what this does to the contrasts. Also: I am conducting a project in which one component has a strong allometric component (bodysize explains 94% of variance). I am trying to generate a LSR of this variable(y) on a second factor (x) to check for correlation. If I calculate residuals (nonphylogenetically, from tip data) for the y component, create contrasts for those residuals and for the raw x variable, standardized these contrasts and then regress y on x, I get a significant correlation (p=0.48, significant, but not impressive). If instead I generate contrasts for each variable-x, bodysize, and y-and then run a multiple regression (with bodymass on the x axis), I find no additive component from the target x variable. Is there a reason to prefer one method over the other? Hope this wasn't too confusing. Thanks! >________________ >_______________________________________________ >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/20100303/0810566d/attachment.html From g.ybazeta at utoronto.ca Mon Mar 8 13:46:36 2010 From: g.ybazeta at utoronto.ca (Gustavo Ybazeta) Date: Mon, 8 Mar 2010 13:46:36 -0800 Subject: [Mesquitelist] Mesquite crash Message-ID: <201003081346.36960.g.ybazeta@utoronto.ca> Hello, I just installed Mesquite on my Linux laptop. However, when it was booting (see: Mesquite_log) crashed but not only the program but the entire system (very unusual) taking me back to the login access to the computer. Any ideas? Cheers Gustavo --- Linux system: Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC 2010 (Ubuntu 2.6.31-20.57-generic) Java version: java version "1.6.0_15" Java(TM) SE Runtime Environment (build 1.6.0_15-b03) Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) Mesquite_log: Mesquite version 2.72 (build 527) Copyright (c) 1997-2009 W. Maddison and D. Maddison The basic Mesquite package (class library and basic modules) is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License. Mesquite is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. For details on license and lack of warranty see the GNU Lesser General Public License by selecting "Display License" from the Window menu or at www.gnu.org Principal Authors: Wayne Maddison & David Maddison Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver Development Team Alumnus: Danny Mandel Sat Mar 06 22:11:12 PST 2010 Running under Java 1.6.0_15; virtual machine by Sun Microsystems Inc. on Linux 2.6.31-20-generic (architecture: i386) User: gustavo Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ commons- httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip commons-codec-1.3.jar commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar iText.jar Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ Log file located in: /home/gustavo/Mesquite_Support_Files Prefs directory: /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs Modules loading from directory /home/gustavo/Programs/Mesquite_Folder/./mesquite/ ancstates basic categ charMatrices charts cont genesis io lists minimal parsimony stochchar trees align assoc batchArch coalesce (CRASH!) From kwhitney at rice.edu Mon Mar 8 17:14:34 2010 From: kwhitney at rice.edu (Ken Whitney) Date: Mon, 08 Mar 2010 19:14:34 -0600 Subject: [Mesquitelist] Parsimony Ancestral States Message-ID: <4B95A0FA.3070106@rice.edu> Hello all, As a visual heuristic, I am using the Parsimony Ancestral States method to trace a character on a phylogeny with arbitrary branch lengths. I would like to understand better how the method works. Specifically, what branch lengths are being assumed when branch lengths are unspecified? How are branch lengths used in the calculations? Is there a good paper to read/cite? Many thanks, Ken Whitney -- ------------------ Ken Whitney Assistant Professor Dept. of Ecology and Evolutionary Biology Rice University Houston, TX 77005 USA 713 348 3057 http://www.ruf.rice.edu/~kwhitney/ From cozzuol at icb.ufmg.br Tue Mar 9 10:01:11 2010 From: cozzuol at icb.ufmg.br (Mario Alberto Cozzuol) Date: Tue, 09 Mar 2010 15:01:11 -0300 Subject: [Mesquitelist] Mesquite crash In-Reply-To: <201003081346.36960.g.ybazeta@utoronto.ca> References: <201003081346.36960.g.ybazeta@utoronto.ca> Message-ID: <1268157671.3207.5.camel@paleo-laptop> Hi, I have the same problem. It seems be related to the use of Compiz or some composite windows manager, apparently incompatible with Mesquite, but I am not sure. However, I use Compiz a long time ago and Mesquite start to crash relative recently (abou 3 month ago). I will like to see a solution for this. Mario -- Dr. Mario Alberto Cozzuol Sala B2-246 Departamento de Zoologia Instituto de Ci?ncias Biol?gicas Universidade Federal de Minas Gerais Av. Ant?nio Carlos, 6627 - Pampulha 31270-910, Belo Horizonte, MG Tel. (31) 3409-2911 E-mail: cozzuol at icb.ufmg.br On Mon, 2010-03-08 at 13:46 -0800, Gustavo Ybazeta wrote: > Hello, > > I just installed Mesquite on my Linux laptop. However, when it was booting > (see: Mesquite_log) crashed but not only the program but the entire system > (very unusual) taking me back to the login access to the computer. Any ideas? > > Cheers > > Gustavo > > --- > > Linux system: > > Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 (Ubuntu > 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC 2010 (Ubuntu > 2.6.31-20.57-generic) > > Java version: > java version "1.6.0_15" > Java(TM) SE Runtime Environment (build 1.6.0_15-b03) > Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) > > Mesquite_log: > Mesquite version 2.72 (build 527) > Copyright (c) 1997-2009 W. Maddison and D. Maddison > The basic Mesquite package (class library and basic modules) is free software; > you can redistribute it and/or modify it under the terms of the GNU Lesser > General Public License. Mesquite is distributed in the hope that it will be > useful, but WITHOUT ANY WARRANTY. For details on license and lack of warranty > see the GNU Lesser General Public License by selecting "Display License" from > the Window menu or at www.gnu.org > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > Sat Mar 06 22:11:12 PST 2010 > Running under Java 1.6.0_15; virtual machine by Sun Microsystems Inc. on Linux > 2.6.31-20-generic (architecture: i386) > User: gustavo > > Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ commons- > httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip commons-codec-1.3.jar > commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar iText.jar > > > Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ > Log file located in: /home/gustavo/Mesquite_Support_Files > Prefs directory: /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory > /home/gustavo/Programs/Mesquite_Folder/./mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch coalesce (CRASH!) > > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From cozzuol at icb.ufmg.br Tue Mar 9 10:02:00 2010 From: cozzuol at icb.ufmg.br (Mario Alberto Cozzuol) Date: Tue, 09 Mar 2010 15:02:00 -0300 Subject: [Mesquitelist] crash Xorg during Mesquite starts In-Reply-To: <86bb4e3b1002251213o74d2d6e1x20b6a970b82472ed@mail.gmail.com> References: <86bb4e3b1002251213o74d2d6e1x20b6a970b82472ed@mail.gmail.com> Message-ID: <1268157720.3207.6.camel@paleo-laptop> Same problem here. See Gustavo Ybazeta post above. Mario -- Dr. Mario Alberto Cozzuol Sala B2-246 Departamento de Zoologia Instituto de Ci?ncias Biol?gicas Universidade Federal de Minas Gerais Av. Ant?nio Carlos, 6627 - Pampulha 31270-910, Belo Horizonte, MG Tel. (31) 3409-2911 E-mail: cozzuol at icb.ufmg.br On Thu, 2010-02-25 at 17:13 -0300, Alejo C.S. wrote: > Dear all, I'm using Mesquite 2.72 on Debian Squeeze (amd64) and Sun > Java 1.6.0_18 in KDE 4.3.4 desktop environment. When the program is > starting, suddenly my xserver (Xorg) crash and restarts from login > screen. Nothing appears in the logs (system.log, Xorg.log, kdm.log). > The odd thing is when using OpenJDK Runtime Environment (IcedTea6 1.7) > (6b17-1.7-1) Mesquite starts perfect, but the functionality is awful. > I've redirected the console output in the moment I run Mesquite to txt > file, here is the point where all crash: > > > Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter > Midford, Jeff Oliver > Development Team Alumnus: Danny Mandel > > Thu Feb 25 16:54:34 ART 2010 > Running under Java 1.6.0_18; virtual machine by Sun > Microsystems Inc. on Linux 2.6.32-trunk-amd64 (architecture: > amd64) > User: marmokh > > Incorporated from /home/marmokh/Programas/Mesquite_Folder/./ > dom4j-1.6.1.jar iText.jar commons-logging-1.1.1.jar JSci.zip > commons-lang-2.3.jar commons-codec-1.3.jar Jama-1.0.1.zip > pal.zip commons-httpclient-3.1.jar > > Mesquite directory: /home/marmokh/Programas/Mesquite_Folder/./ > Log file located in: /home/marmokh/Mesquite_Support_Files > Prefs > directory: /home/marmokh/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from > directory /home/marmokh/Programas/Mesquite_Folder/./mesquite/ > > ancstates basic categ charMatrices charts cont genesis io > lists minimal parsimony stochchar trees align assoc batchArch > > > It seems that after loading the package batchArch the system crash. > One thing that I'm very confused is that in my home computer I have > the same system (Debian amd64 Squeeze and KDE4) and mesquite runs just > fine with sun JAVA. My home computer works with a nvidia video card > and my work computer (where is the problem) runs a intel video card, > maybe that is the problem????. > > Thanks in advance. > > > Alejo > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From g.ybazeta at utoronto.ca Tue Mar 9 19:47:50 2010 From: g.ybazeta at utoronto.ca (Gustavo Ybazeta) Date: Tue, 9 Mar 2010 19:47:50 -0800 Subject: [Mesquitelist] Mesquite crash In-Reply-To: <1268157671.3207.5.camel@paleo-laptop> References: <201003081346.36960.g.ybazeta@utoronto.ca> <1268157671.3207.5.camel@paleo-laptop> Message-ID: <201003091947.50862.g.ybazeta@utoronto.ca> Hello, I am not sure it is something to do with Compiz. I don't have this program installed and I disable all desktop effect and still the same problem. Gustavo PS: by the way my video card is intel too... perhaps... On March 9, 2010 10:01:11 am Mario Alberto Cozzuol wrote: > Hi, > I have the same problem. It seems be related to the use of Compiz or > some composite windows manager, apparently incompatible with Mesquite, > but I am not sure. > However, I use Compiz a long time ago and Mesquite start to crash > relative recently (abou 3 month ago). > I will like to see a solution for this. > > > Mario > > > Hello, > > > > I just installed Mesquite on my Linux laptop. However, when it was > > booting (see: Mesquite_log) crashed but not only the program but the > > entire system (very unusual) taking me back to the login access to the > > computer. Any ideas? > > > > Cheers > > > > Gustavo > > > > --- > > > > Linux system: > > > > Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 > > (Ubuntu 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC 2010 > > (Ubuntu 2.6.31-20.57-generic) > > > > Java version: > > java version "1.6.0_15" > > Java(TM) SE Runtime Environment (build 1.6.0_15-b03) > > Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) > > > > Mesquite_log: > > Mesquite version 2.72 (build 527) > > Copyright (c) 1997-2009 W. Maddison and D. Maddison > > The basic Mesquite package (class library and basic modules) is free > > software; you can redistribute it and/or modify it under the terms of the > > GNU Lesser General Public License. Mesquite is distributed in the hope > > that it will be useful, but WITHOUT ANY WARRANTY. For details on license > > and lack of warranty see the GNU Lesser General Public License by > > selecting "Display License" from the Window menu or at www.gnu.org > > > > Principal Authors: Wayne Maddison & David Maddison > > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff > > Oliver Development Team Alumnus: Danny Mandel > > > > Sat Mar 06 22:11:12 PST 2010 > > Running under Java 1.6.0_15; virtual machine by Sun Microsystems Inc. on > > Linux 2.6.31-20-generic (architecture: i386) > > User: gustavo > > > > Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ commons- > > httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip commons-codec-1.3.jar > > commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar iText.jar > > > > > > Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ > > Log file located in: /home/gustavo/Mesquite_Support_Files > > Prefs directory: /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs > > > > Modules loading from directory > > /home/gustavo/Programs/Mesquite_Folder/./mesquite/ > > > > ancstates basic categ charMatrices charts cont genesis io lists minimal > > parsimony stochchar trees align assoc batchArch coalesce (CRASH!) > > > > > > _______________________________________________ > > Mesquitelist mailing list > > Mesquitelist at mesquiteproject.org > > http://mesquiteproject.org/mailman/listinfo/mesquitelist > -- Gustavo Ybazeta Department of Ecology and & Evolutionary Biology University of Toronto Department of Natural History Royal Ontario Museum g.ybazeta"at"utoronto.ca From Robin.vanVelzen at wur.nl Thu Mar 11 01:14:06 2010 From: Robin.vanVelzen at wur.nl (Velzen, Robin van) Date: Thu, 11 Mar 2010 10:14:06 +0100 Subject: [Mesquitelist] Adding noise to branch lengths Message-ID: <2FD291037C4E874E9D91AF3CDF899D14E1DDAB@scomp0038.wurnet.nl> Dear Mesquite users and developers, I am simulating DNA sequence data on coalescence-based gene trees. To add realistic variance to the simulated data, I wish to introduce branch-length variation using the 'Randomly Modify Current Tree' module. By default,, this sets variance to be proportional to the original branch lengths. However, I would like to set a fixed variance independent to the original branch lengths in order to achieve significant variance in short branches also. Reading the description of the NoiseToBranchLengths module, it should be possible to turn off this proportionality of variance (toggleproport off) but unfortunately there is no equivalent toggle in the Mesquite menu. I then tried scripting the module but this produces the error message "A tree modifier had to quit because it would be attempting to modify its own trees, resulting in an infinite recursion". Any help or suggestion on how I can add random noise to branch lengths with a fixed variance would be very much appreciated! Thanks in advance and with best wishes, Robin Robin van Velzen PhD student Netherlands Centre for Biodiversity 'Naturalis' (section NHN) Biosystematics Group Wageningen University Wageningen Campus, Radix building 107, Room W4.Aa.095 Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands PO Box 647, 6700 AP Wageningen, The Netherlands Tel. +31 (0)317 483425 http://www.bis.wur.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100311/c5ea8b75/attachment.html From wmaddisn at interchange.ubc.ca Sun Mar 14 13:20:05 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:20:05 -0800 Subject: [Mesquitelist] apologies Message-ID: Apologies for the long delay in responding to Mesquite questions. We'll be answering the queries from the last several weeks shortly. -- ---------------------------------------------------------------------------- Wayne Maddison David R. Maddison Departments of Zoology and Botany Department of Zoology University of British Columbia 3029 Cordley Hall Vancouver, BC V6T 1Z4 Oregon State University Corvallis, OR 97331 email: wmaddisn at interchange.ubc.ca david.maddison at science.oregonstate.edu Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Tree of Life: http://tolweb.org From wmaddisn at interchange.ubc.ca Sun Mar 14 13:22:14 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:22:14 -0800 Subject: [Mesquitelist] Mesquite 2.72 , Kubuntu 9.04 and Sun Java 6. In-Reply-To: <9674ce851002220625g3368e3b3h50cfa8abd94da971@mail.gmail.com> References: <9674ce851002220625g3368e3b3h50cfa8abd94da971@mail.gmail.com> Message-ID: It seems as if you have incompatible modules installed. Do you have any extra packages (e.g. PDAP) installed? If so you need to ensure they are up to date. Could you send straight to me the Mesquite_Log file that is in Mesquite_Support_Files after this happens? Thanks, Wayne At 11:25 AM -0300 22.2.2010, Fl?vio Uemori Yamamoto wrote: >Hello. >This is my first e-mail to this list. > >I was using Mesquite version 2.6 (everything ok) >and recently upgraded to version 2.72. >Now, when I start the program, it opens a "crash" box with the message below: > >"There has been a problem starting a module (class >java.lang.NoSuchFieldError). This may be the result of an old, >incompatible package being used, or part of Mesquite was >accidentally deleted. (module: Defaults; arguments: null; module >being started: mesquite.minimal.Defaults.Defaults; ERROR: >storedAsDefault; error class class java.lang.NoSuchFieldError [2])" > >My computer runs Linux Kubuntu 9.04 and has the java package "Sun >Java(TM) Runtime Environment (JRE) 6". >What am I doing wrong? >Thank you. >Best regards. > >Fl?vio Uemori Yamamoto > >Laborat?rio de Artr?podes, Instituto Butantan >Av. Vital Brasil, 1500 >05503-900 - S?o Paulo - SP - Brazil >Telefone: 005511 3726-7222 ramal: 2235, 2180 > >_______________________________________________ >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 Mar 14 13:23:32 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:23:32 -0800 Subject: [Mesquitelist] differentiation between mesquite and DIVA In-Reply-To: <626001.84278.qm@web113905.mail.gq1.yahoo.com> References: <626001.84278.qm@web113905.mail.gq1.yahoo.com> Message-ID: Mesquite has various models for use with parsimony, but none match DIVA's. Mesquite's current parsimony models are designed for phenotypic character states that are typically assumed never to be polymorphic. In the case of geography, it is assumed a lineage can exist in more than one area at once. Just as the results differ when using ordered, unordered and stepmatrix assumptions with phenotypic characters, the results differ from any of those and DIVA, which uses very different assumptions. Wayne >Dear All, > >I used mesquite and DIVA to reconstract the distribution range of >nodes for my data set . In some cases I have different results >(according to both of them are pasimony-based method). I would like >to know the differentiation between these two programs. > >I guess the differrentiation is due to in Mesquite none of the >biogeographical events (vicariance, dispersal, etc.) have any cost, >although vicariance is the null model in DIVA. > >I am right? > >Any help is appreciated. > > > >Thanks > >Sara > > > > > > > >_______________________________________________ >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 Mar 14 13:23:51 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:23:51 -0800 Subject: [Mesquitelist] Simple question In-Reply-To: <686090a71002241351h12448418mb4efa295aa100fbe@mail.gmail.com> References: <686090a71002241351h12448418mb4efa295aa100fbe@mail.gmail.com> Message-ID: At 10:51 PM +0100 24.2.2010, S?bastien Patiny wrote: >Hi all, > >What are the taxon 100000 >and character limits in Mesquite? there is no explicit limit. But, you may run out of memory if you make a matrix too big. Wayne > >Best, >Seb > >-- >---------------------------------------------------- >Dr S?bastien Patiny >(Entomologist) >Chemcom s.a. >1070 Brussels >BELGIUM > >url : >http://sites.google.com/site/patinys/ > >_______________________________________________ >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 Mar 14 13:24:12 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:24:12 -0800 Subject: [Mesquitelist] Mesquite crash In-Reply-To: <201003091947.50862.g.ybazeta@utoronto.ca> References: <201003081346.36960.g.ybazeta@utoronto.ca> <1268157671.3207.5.camel@paleo-laptop> <201003091947.50862.g.ybazeta@utoronto.ca> Message-ID: This is quite a mystery to us. Being a simple pure java program, Mesquite itself should be unable to crash anything, much less your login. This must be a bug somehwere in java, KDE, linux -- that is, outside of Mesquite. If any of you figure out how to fix the problem with your systems (e.g. turning off graphics accelleration??) then please post on this list to share. Wayne At 7:47 PM -0800 9.3.2010, Gustavo Ybazeta wrote: >Hello, > >I am not sure it is something to do with Compiz. I don't have this program >installed and I disable all desktop effect and still the same problem. > >Gustavo > >PS: by the way my video card is intel too... perhaps... > > >On March 9, 2010 10:01:11 am Mario Alberto Cozzuol wrote: >> Hi, >> I have the same problem. It seems be related to the use of Compiz or >> some composite windows manager, apparently incompatible with Mesquite, >> but I am not sure. >> However, I use Compiz a long time ago and Mesquite start to crash >> relative recently (abou 3 month ago). >> I will like to see a solution for this. >> >> >> Mario >> >> > Hello, >> > >> > I just installed Mesquite on my Linux laptop. However, when it was >> > booting (see: Mesquite_log) crashed but not only the program but the >> > entire system (very unusual) taking me back to the login access to the >> > computer. Any ideas? >> > >> > Cheers >> > >> > Gustavo >> > >> > --- >> > >> > Linux system: >> > >> > Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 >> > (Ubuntu 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC 2010 >> > (Ubuntu 2.6.31-20.57-generic) >> > >> > Java version: >> > java version "1.6.0_15" >> > Java(TM) SE Runtime Environment (build 1.6.0_15-b03) >> > Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) >> > >> > Mesquite_log: >> > Mesquite version 2.72 (build 527) >> > Copyright (c) 1997-2009 W. Maddison and D. Maddison >> > The basic Mesquite package (class library and basic modules) is free >> > software; you can redistribute it and/or modify it under the terms of the >> > GNU Lesser General Public License. Mesquite is distributed in the hope >> > that it will be useful, but WITHOUT ANY WARRANTY. For details on license >> > and lack of warranty see the GNU Lesser General Public License by >> > selecting "Display License" from the Window menu or at www.gnu.org >> > >> > Principal Authors: Wayne Maddison & David Maddison >> > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff >> > Oliver Development Team Alumnus: Danny Mandel >> > >> > Sat Mar 06 22:11:12 PST 2010 >> > Running under Java 1.6.0_15; virtual machine by Sun Microsystems Inc. on >> > Linux 2.6.31-20-generic (architecture: i386) >> > User: gustavo >> > >> > Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ commons- >> > httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip commons-codec-1.3.jar >> > commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar iText.jar >> > >> > >> > Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ >> > Log file located in: /home/gustavo/Mesquite_Support_Files >> > Prefs directory: /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs >> > >> > Modules loading from directory >> > /home/gustavo/Programs/Mesquite_Folder/./mesquite/ >> > >> > ancstates basic categ charMatrices charts cont genesis io lists minimal >> > parsimony stochchar trees align assoc batchArch coalesce (CRASH!) >> > >> > >> > _______________________________________________ >> > Mesquitelist mailing list >> > Mesquitelist at mesquiteproject.org >> > http://mesquiteproject.org/mailman/listinfo/mesquitelist >> > >-- >Gustavo Ybazeta > >Department of Ecology and & Evolutionary Biology >University of Toronto >Department of Natural History >Royal Ontario Museum > >g.ybazeta"at"utoronto.ca >_______________________________________________ >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 Mar 14 13:24:22 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:24:22 -0800 Subject: [Mesquitelist] Adding noise to branch lengths In-Reply-To: <2FD291037C4E874E9D91AF3CDF899D14E1DDAB@scomp0038.wurnet.nl> References: <2FD291037C4E874E9D91AF3CDF899D14E1DDAB@scomp0038.wurnet.nl> Message-ID: There should be a menu item that appears once the Add Noise to Branch Lengths module is started -- perhaps check again? We'll have a fix for the "infinite recursion" problem in the next release of Mesquite. If any of you need the fix sooner please say. Wayne At 10:14 AM +0100 11.3.2010, Velzen, Robin van wrote: >Content-type: multipart/alternative; > boundary="Boundary_(ID_nb1cl4Wcd+aWS/EcXinM+g)" >Content-class: urn:content-classes:message > >Dear Mesquite users and developers, > >I am simulating DNA sequence data on coalescence-based gene trees. >To add realistic variance to the simulated data, I wish to introduce >branch-length variation using the 'Randomly Modify Current Tree' >module. By default,, this sets variance to be proportional to the >original branch lengths. However, I would like to set a fixed >variance independent to the original branch lengths in order to >achieve significant variance in short branches also. > >Reading the description of the NoiseToBranchLengths module, it >should be possible to turn off this proportionality of variance >(toggleproport off) but unfortunately there is no equivalent toggle >in the Mesquite menu. I then tried scripting the module but this >produces the error message "A tree modifier had to quit because it >would be attempting to modify its own trees, resulting in an >infinite recursion". > >Any help or suggestion on how I can add random noise to branch >lengths with a fixed variance would be very much appreciated! > >Thanks in advance and with best wishes, > >Robin > > >Robin van Velzen >PhD student >Netherlands Centre for Biodiversity 'Naturalis' (section NHN) >Biosystematics Group >Wageningen University > >Wageningen Campus, Radix building 107, Room W4.Aa.095 >Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands >PO Box 647, 6700 AP Wageningen, The Netherlands >Tel. +31 (0)317 483425 >http://www.bis.wur.nl > > >_______________________________________________ >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 Mar 14 13:24:50 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:24:50 -0800 Subject: [Mesquitelist] importing tree for matrix In-Reply-To: References: Message-ID: At 6:22 PM +0000 26.2.2010, m. candida wrote: >I have a matrix with X taxa. In order to run IC tests for the >characters I need to import a tree. So, two questions: > >1. How can I import a tree so that it is associated with my matrix? If the tree and matrix use the same taxon names then you can open the one file first, then ask to include the other file (File>Include FIle...). >2. Do I need to manually clip those taxa from the tree that are not >in my matrix? No, as long as you open the tree file first and then the matrix. Wayne > > >Any advice would be appreciated. > >Eric > > >Hotmail: Free, trusted and rich email service. >Get it now. > >_______________________________________________ >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 Mar 14 13:26:15 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 14 Mar 2010 12:26:15 -0800 Subject: [Mesquitelist] Parsimony Ancestral States In-Reply-To: <4B95A0FA.3070106@rice.edu> References: <4B95A0FA.3070106@rice.edu> Message-ID: If you are using categorical data, then the branch lengths are not used at all in the parsimony calculations. In general parsimony methods don't use branch lengths. The only "parsimony" calculations that use branch lengths are those for squared change parsimony for continuous valued data. Does that answer your question? Wayne At 7:14 PM -0600 8.3.2010, Ken Whitney wrote: >Hello all, > >As a visual heuristic, I am using the Parsimony Ancestral States method >to trace a character on a phylogeny with arbitrary branch lengths. I >would like to understand better how the method works. Specifically, >what branch lengths are being assumed when branch lengths are >unspecified? How are branch lengths used in the calculations? Is there >a good paper to read/cite? > >Many thanks, >Ken Whitney > >-- >------------------ >Ken Whitney >Assistant Professor >Dept. of Ecology and Evolutionary Biology >Rice University >Houston, TX 77005 USA >713 348 3057 >http://www.ruf.rice.edu/~kwhitney/ > >_______________________________________________ >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 awehe at iastate.edu Sun Mar 14 13:26:34 2010 From: awehe at iastate.edu (Andre Wehe) Date: Sun, 14 Mar 2010 16:26:34 -0400 Subject: [Mesquitelist] Gene tree parsimony Message-ID: Hello, I am a new user and a little overwhelmed with Mesquites features. I appreciate some help to guide me once through the menu. I am trying to compare a Mesquite feature with my own implementation. The feature I am looking for is gene tree parsimony where I infer a species tree from a set of gene trees. I already figured Mesquite can do a heuristic search with tree SPR or NNI rearrangements, but I am struggling getting the tree search started for the objectives gene duplications and gene duplications+gene losses. "Deep coalescence Multi-Loci" seems to work for the deep coalescence objective when I have a set of gene trees in a single tree block. It is unclear to me what the other objectives like "Deep coalescence (gene tree)" and "Deep coalescence (species tree)" are for. It might be that I did not get the input right, but they seem to consider only 1 gene tree at a time during a search. Also, is it possible to provide a user specified starting species tree that Mesquite optimizes rather than building a new species tree from scratch? Thanks in advance, -- Andre -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100314/d2f8d154/attachment.html From david.maddison at science.oregonstate.edu Mon Mar 15 17:23:25 2010 From: david.maddison at science.oregonstate.edu (David Maddison) Date: Mon, 15 Mar 2010 17:23:25 -0700 Subject: [Mesquitelist] numbers of MPRs In-Reply-To: <57d1a1d51002241846k1b4ab98av9c2a957a13098a95@mail.gmail.com> References: <57d1a1d51002241846k1b4ab98av9c2a957a13098a95@mail.gmail.com> Message-ID: There are some trees that have an incredibly large number of equally most parsimonious reconstructions of character evolution, more than the maximum number allowed for an integer in Java. This may be your problem, in which case there is not much that can be done about it. Or, it may be that you have encountered a bug in Mesquite. If you send to me directly a copy of your file that illustrates this problem, I can check. Thanks, David On 24 Feb 2010, at 6:46 PM, Yi Kong wrote: > Hi everybody, > > I meet an problem in parsimony reconstruction when I click Summaries State Changes over trees, > > this dialog box appears, > "Number of MPRs exceeds that allowed - calculations can not be completed." > > Who can tell me how to reslove it? > > Thanks a lot! > -- > Yi Kong > P.O. BOX159 > No.1 Wenyuan road, > College of Life Science, > Nanjing Normal University, > Nanjing, Jiangsu province 210046, > P.R. China > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From david.maddison at science.oregonstate.edu Mon Mar 15 17:27:17 2010 From: david.maddison at science.oregonstate.edu (David Maddison) Date: Mon, 15 Mar 2010 17:27:17 -0700 Subject: [Mesquitelist] full distribution of number of changes In-Reply-To: <20100208154112.14457jwyfnz82mio@webmail.urjc.es> References: <4B6FF8F2.7080407@uj.edu.pl> <20100208154112.14457jwyfnz82mio@webmail.urjc.es> Message-ID: <7AA69EB8-0F91-4183-95AB-3EAC70C2F8F3@science.oregonstate.edu> Ana, In the Summarize_Changes menu, there is the option Maximum Number of Changed Recorded. If you choose that, you can adjust the number to more than 9. Best wishes, David On 8 Feb 2010, at 6:41 AM, ana.millanes at urjc.es wrote: > Hello, > > I'd be grateful for any advice: > > I'm counting the amount of change in a character over a tree sample > with Mesquite (using "Analyze"-"Other Analyses with trees"-"Summarize > change in selected clade" > > I would like to obtain the full distribution of the number of changes > across the tree sample (i. e., X trees say there was 1 change, Y trees > there were 2 changes, etc). > > In the way I'm doing it I get the fraction of trees predicting each > change value (from 0 to 9) but all the trees predicting 10 or more > changes are included in the same category (10+) > > Is there any way to tell the program to output the information on the > full distribution? > > Many thanks in advance, > > Ana > > > Ana Mar?a Millanes Romero > Departamental 1 DI-210 > Departamento de Biolog?a y Geolog?a (ESCET) > Universidad Rey Juan Carlos > C/ Tulip?n, s/n > E-28933 M?stoles, Madrid > Phone: (+34) 914888290 > E-mail: ana.millanes at urjc.es > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From kipwill at berkeley.edu Wed Mar 17 21:54:12 2010 From: kipwill at berkeley.edu (Kipling (Kip) Will) Date: Wed, 17 Mar 2010 21:54:12 -0700 Subject: [Mesquitelist] Compress Characters command? In-Reply-To: <7AA69EB8-0F91-4183-95AB-3EAC70C2F8F3@science.oregonstate.edu> References: <4B6FF8F2.7080407@uj.edu.pl> <20100208154112.14457jwyfnz82mio@webmail.urjc.es> <7AA69EB8-0F91-4183-95AB-3EAC70C2F8F3@science.oregonstate.edu> Message-ID: <4BA1B1F4.6070105@berkeley.edu> Does Mesquite have an equivalent command to the "Compress Characters" command as implemented in Macclade? If so, please point me to it. best, 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 herpgirl at gmail.com Fri Mar 19 08:48:34 2010 From: herpgirl at gmail.com (Allyson Fenwick) Date: Fri, 19 Mar 2010 11:48:34 -0400 Subject: [Mesquitelist] BiSSE and constraining parameter values Message-ID: <1c0342481003190848k510dae46l30be2a5d777b3439@mail.gmail.com> Hi all, I am in the process of testing multiple models of character evolution with BiSSE likelihood. It's worked fine for 8 models where I constrain parameters to be equal to each other or to vary freely, and it works with using the script for multiple trees, but now that I'm running models that require me to set one parameter equal to 0, the process fails for the vast majority of the trees. A sample error looks like this: (BiSSE Parameters) # (Mesquite) # Estimating model with parameters ? =1 ? =0 ? =3 ? =2 ? 0.0 BiSSE calculations: Tree STATE 1002000 and character Character 1 BiSSE calculations: Estimating 5 free parameters BiSSE calculations: Estimating parameters, phase 1: step count 100 BiSSE calculations: random attempt 1 failed because starting position had undefined likelihood ... BiSSE calculations: attempt failed because starting position had undefined likelihood BiSSE calculations: Estimating parameters failed I have 2000 trees and 1 binary character to track, a character that is unknown or has multiple states for 4 species. I edited the treefiles generated in BEAST to add an outgroup with very short branch lengths (to constrain the root node to a particular character state). Thanks in advance for any help! Allyson From oakley at lifesci.ucsb.edu Fri Mar 19 08:52:47 2010 From: oakley at lifesci.ucsb.edu (Todd Oakley) Date: Fri, 19 Mar 2010 08:52:47 -0700 Subject: [Mesquitelist] BiSSE and constraining parameter values In-Reply-To: <1c0342481003190848k510dae46l30be2a5d777b3439@mail.gmail.com> References: <1c0342481003190848k510dae46l30be2a5d777b3439@mail.gmail.com> Message-ID: <4BA39DCF.3040109@lifesci.ucsb.edu> Allyson, I'm doing the exact same thing. I've just been setting the rates VERY low to approximate zero. Values like 0.0000001 Todd > Hi all, > > I am in the process of testing multiple models of character evolution > with BiSSE likelihood. It's worked fine for 8 models where I constrain > parameters to be equal to each other or to vary freely, and it works > with using the script for multiple trees, but now that I'm running > models that require me to set one parameter equal to 0, the process > fails for the vast majority of the trees. > > A sample error looks like this: > (BiSSE Parameters) # > (Mesquite) # Estimating model with parameters ? =1 ? =0 ? =3 ? =2 ? 0.0 > BiSSE calculations: Tree STATE 1002000 and character Character 1 > BiSSE calculations: Estimating 5 free parameters > BiSSE calculations: Estimating parameters, phase 1: step count 100 > BiSSE calculations: random attempt 1 failed because starting position > had undefined likelihood > ... > BiSSE calculations: attempt failed because starting position had > undefined likelihood > BiSSE calculations: Estimating parameters failed > > I have 2000 trees and 1 binary character to track, a character that is > unknown or has multiple states for 4 species. I edited the treefiles > generated in BEAST to add an outgroup with very short branch lengths > (to constrain the root node to a particular character state). > > Thanks in advance for any help! > Allyson > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist > -- ________________________________________ Todd H. Oakley Professor Ecology Evolution and Marine Biology University of California-Santa Barbara Santa Barbara, CA 93106 (805) 893-4715 http://www.lifesci.ucsb.edu/eemb/labs/oakley/ From adrian.down at gmail.com Tue Mar 23 09:55:18 2010 From: adrian.down at gmail.com (Adrian) Date: Tue, 23 Mar 2010 12:55:18 -0400 Subject: [Mesquitelist] Change location of "Mesquite_Support_Files" folder? Message-ID: <5db859a1003230955p7af478f0p6fd6ff0d32fb506b@mail.gmail.com> Hello, Is there a way to change the default location of the "Mesquite_Support_Files" folder? I apologize if this is not the correct forum in which to post this question. Thanks, Adrian Down Research Assistant Duke University department of Biology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100323/600fc977/attachment.html From alexander.kupfer at uni-jena.de Thu Mar 25 07:15:22 2010 From: alexander.kupfer at uni-jena.de (Alexander Kupfer) Date: Thu, 25 Mar 2010 15:15:22 +0100 Subject: [Mesquitelist] PICs and real divergence times Message-ID: Dear all, I am analysing the evolution of parental investment in amphibians in a compararative approach using PICs. Well, for many taxa divergence times were estimated in current phylogenies. I would very much use these estimates as real branch lengths in my comparative analysis. But how do I type estimates in millions of years into mesquite i.e. in which format are they entered? Can someone help? With kind regards Alex PS I am using a Mac (MacOS 10.5) and Mesquite 2.6 ============================================= Dr Alexander Kupfer ?? Institut f?r Spezielle Zoologie und Evolutionsbiologie mit Phyletischem Museum Friedrich-Schiller-Universit?t Jena Erbertstr. 1 07743 Jena Germany ???? Tel ????????+49 (0) 3641 949183 Fax ???????+49 (0) 3641 949162 alexander.kupfer at uni-jena.de alexk at nhm.ac.uk or alexkupfer at yahoo.de ??? http://www.uni-jena.de/szeb.html http://www.phyletisches-museum.uni-jena.de/ ? ============================================= From michel.laurin at upmc.fr Thu Mar 25 07:25:47 2010 From: michel.laurin at upmc.fr (Michel Laurin) Date: Thu, 25 Mar 2010 15:25:47 +0100 Subject: [Mesquitelist] PICs and real divergence times In-Reply-To: References: Message-ID: <4BAB726B.1070102@upmc.fr> Dear Alexander, You can directly type in the number of millions of years into Mesquite using one of the tools (left column, seventh from top) in a tree window. To see the results, you need to select "Branches proportional to length" in the drawing menu. However, if you use the paleontological literature to estimate divergence times from the fossil record, you might find the optional Stratigraphic Tools package useful (you can download it from the Mesquite download page). I published a rather detailed study of timing of diversification in lissamphibians using that module, and you may perhaps find it useful for your study: Marjanovi?, D. & Laurin, M. (2007) Systematic Biology 56, 369-388. Cheers, Michel On 25/03/10 15:15, Alexander Kupfer wrote: > Dear all, > I am analysing the evolution of parental investment in amphibians in a > compararative approach using PICs. > > Well, for many taxa divergence times were estimated in current phylogenies. > I would very much use these estimates as real branch lengths in my > comparative analysis. > > But how do I type estimates in millions of years into mesquite i.e. in which > format are they entered? > > Can someone help? > > With kind regards > > Alex > > PS I am using a Mac (MacOS 10.5) and Mesquite 2.6 > ============================================= > > Dr Alexander Kupfer > > Institut f?r Spezielle Zoologie und Evolutionsbiologie > mit Phyletischem Museum > Friedrich-Schiller-Universit?t Jena > Erbertstr. 1 > 07743 Jena > Germany > > Tel +49 (0) 3641 949183 > Fax +49 (0) 3641 949162 > > alexander.kupfer at uni-jena.de > alexk at nhm.ac.uk or alexkupfer at yahoo.de > > http://www.uni-jena.de/szeb.html > http://www.phyletisches-museum.uni-jena.de/ > > ============================================= > > > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist > > From david.maddison at science.oregonstate.edu Sat Mar 27 19:03:24 2010 From: david.maddison at science.oregonstate.edu (David Maddison) Date: Sat, 27 Mar 2010 19:03:24 -0700 Subject: [Mesquitelist] Compress Characters command? In-Reply-To: <4BA1B1F4.6070105@berkeley.edu> References: <4B6FF8F2.7080407@uj.edu.pl> <20100208154112.14457jwyfnz82mio@webmail.urjc.es> <7AA69EB8-0F91-4183-95AB-3EAC70C2F8F3@science.oregonstate.edu> <4BA1B1F4.6070105@berkeley.edu> Message-ID: <44C64CD8-46AB-42F8-8926-7B8AA887F07D@science.oregonstate.edu> I don't think so. It shouldn't be too hard for someone to add it, though. David On 17 Mar 2010, at 9:54 PM, Kipling (Kip) Will wrote: > Does Mesquite have an equivalent command to the "Compress Characters" > command as implemented in Macclade? If so, please point me to it. > > best, > 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 From jeffrey.oliver at yale.edu Mon Mar 29 11:36:54 2010 From: jeffrey.oliver at yale.edu (Jeffrey C. Oliver) Date: Mon, 29 Mar 2010 14:36:54 -0400 Subject: [Mesquitelist] Mesquite crash in Linux Message-ID: This is likely a java virtual machine problem: when running Mesquite via java-6-sun1.6.0.16, Linux restarts* while loading modules. However, when using java-6-openjdk, Mesquite works just fine. Older versions of sun's java might work, but I've not tested them myself. -Jeff *Technically, it's not a full restart, Linux just closes all open programs, logs the current user out, and returns to the login screen. On Sun, Mar 14, 2010 at 4:24 PM, Wayne Maddison wrote: > This is quite a mystery to us. Being a simple pure java program, > Mesquite itself should be unable to crash anything, much less your > login. This must be a bug somehwere in java, KDE, linux -- that is, > outside of Mesquite. > > If any of you figure out how to fix the problem with your systems > (e.g. turning off graphics accelleration??) then please post on this > list to share. > > Wayne > > > At 7:47 PM -0800 9.3.2010, Gustavo Ybazeta wrote: > >Hello, > > > >I am not sure it is something to do with Compiz. I don't have this program > >installed and I disable all desktop effect and still the same problem. > > > >Gustavo > > > >PS: by the way my video card is intel too... perhaps... > > > > > >On March 9, 2010 10:01:11 am Mario Alberto Cozzuol wrote: > >> Hi, > >> I have the same problem. It seems be related to the use of Compiz or > >> some composite windows manager, apparently incompatible with Mesquite, > >> but I am not sure. > >> However, I use Compiz a long time ago and Mesquite start to crash > >> relative recently (abou 3 month ago). > >> I will like to see a solution for this. > >> > >> > >> Mario > >> > >> > Hello, > >> > > >> > I just installed Mesquite on my Linux laptop. However, when it was > >> > booting (see: Mesquite_log) crashed but not only the program but the > >> > entire system (very unusual) taking me back to the login access to > the > >> > computer. Any ideas? > >> > > >> > Cheers > >> > > >> > Gustavo > >> > > >> > --- > >> > > >> > Linux system: > >> > > >> > Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 > >> > (Ubuntu 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC 2010 > >> > (Ubuntu 2.6.31-20.57-generic) > >> > > >> > Java version: > >> > java version "1.6.0_15" > >> > Java(TM) SE Runtime Environment (build 1.6.0_15-b03) > >> > Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) > >> > > >> > Mesquite_log: > >> > Mesquite version 2.72 (build 527) > >> > Copyright (c) 1997-2009 W. Maddison and D. Maddison > >> > The basic Mesquite package (class library and basic modules) is free > >> > software; you can redistribute it and/or modify it under the terms of > the > >> > GNU Lesser General Public License. Mesquite is distributed in the > hope > >> > that it will be useful, but WITHOUT ANY WARRANTY. For details on > license > >> > and lack of warranty see the GNU Lesser General Public License by > >> > selecting "Display License" from the Window menu or at www.gnu.org > >> > > >> > Principal Authors: Wayne Maddison & David Maddison > >> > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff > >> > Oliver Development Team Alumnus: Danny Mandel > >> > > >> > Sat Mar 06 22:11:12 PST 2010 > >> > Running under Java 1.6.0_15; virtual machine by Sun Microsystems Inc. > on > >> > Linux 2.6.31-20-generic (architecture: i386) > >> > User: gustavo > >> > > >> > Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ commons- > >> > httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip > commons-codec-1.3.jar > >> > commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar > iText.jar > >> > > >> > > >> > Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ > >> > Log file located in: /home/gustavo/Mesquite_Support_Files > >> > Prefs directory: /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs > >> > > >> > Modules loading from directory > >> > /home/gustavo/Programs/Mesquite_Folder/./mesquite/ > >> > > >> > ancstates basic categ charMatrices charts cont genesis io lists > minimal > >> > parsimony stochchar trees align assoc batchArch coalesce (CRASH!) > >> > > >> > > >> > _______________________________________________ > >> > Mesquitelist mailing list > >> > Mesquitelist at mesquiteproject.org > >> > http://mesquiteproject.org/mailman/listinfo/mesquitelist > >> > > > >-- > >Gustavo Ybazeta > > > >Department of Ecology and & Evolutionary Biology > >University of Toronto > >Department of Natural History > >Royal Ontario Museum > > > >g.ybazeta"at"utoronto.ca > >_______________________________________________ > >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 > _______________________________________________ > 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/20100329/652a886b/attachment.html From g.ybazeta at utoronto.ca Mon Mar 29 12:40:52 2010 From: g.ybazeta at utoronto.ca (Gustavo Ybazeta) Date: Mon, 29 Mar 2010 12:40:52 -0700 Subject: [Mesquitelist] Mesquite crash in Linux In-Reply-To: References: Message-ID: <201003291240.52444.g.ybazeta@utoronto.ca> Hello Jeff, Thanks, It worked. In Kubuntu I installed openjdk-6-jdk. This version replaced the sun version as a default (It is possible to have both and indicate which version you want for Mesquite). Yes, you were right. Also older versions of sun-java are working. Cheers Gustavo On March 29, 2010 11:36:54 am Jeffrey C. Oliver wrote: > This is likely a java virtual machine problem: when running Mesquite via > java-6-sun1.6.0.16, Linux restarts* while loading modules. However, when > using java-6-openjdk, Mesquite works just fine. Older versions of sun's > java might work, but I've not tested them myself. > > -Jeff > > *Technically, it's not a full restart, Linux just closes all open programs, > logs the current user out, and returns to the login screen. > > On Sun, Mar 14, 2010 at 4:24 PM, Wayne Maddison > > > wrote: > > > > This is quite a mystery to us. Being a simple pure java program, > > Mesquite itself should be unable to crash anything, much less your > > login. This must be a bug somehwere in java, KDE, linux -- that is, > > outside of Mesquite. > > > > If any of you figure out how to fix the problem with your systems > > (e.g. turning off graphics accelleration??) then please post on this > > list to share. > > > > Wayne > > > > At 7:47 PM -0800 9.3.2010, Gustavo Ybazeta wrote: > > >Hello, > > > > > >I am not sure it is something to do with Compiz. I don't have this > > > program installed and I disable all desktop effect and still the same > > > problem. > > > > > >Gustavo > > > > > >PS: by the way my video card is intel too... perhaps... > > > > > >On March 9, 2010 10:01:11 am Mario Alberto Cozzuol wrote: > > >> Hi, > > >> I have the same problem. It seems be related to the use of Compiz or > > >> some composite windows manager, apparently incompatible with > > >> Mesquite, but I am not sure. > > >> However, I use Compiz a long time ago and Mesquite start to crash > > >> relative recently (abou 3 month ago). > > >> I will like to see a solution for this. > > >> > > >> > > >> Mario > > >> > > >> > Hello, > > >> > > > >> > I just installed Mesquite on my Linux laptop. However, when it was > > >> > booting (see: Mesquite_log) crashed but not only the program but > > >> > the entire system (very unusual) taking me back to the login access > > >> > to > > > > the > > > > >> > computer. Any ideas? > > >> > > > >> > Cheers > > >> > > > >> > Gustavo > > >> > > > >> > --- > > >> > > > >> > Linux system: > > >> > > > >> > Linux version 2.6.31-20-generic (buildd at rothera) (gcc version 4.4.1 > > >> > (Ubuntu 4.4.1-4ubuntu9) ) #57-Ubuntu SMP Mon Feb 8 09:05:19 UTC > > >> > 2010 (Ubuntu 2.6.31-20.57-generic) > > >> > > > >> > Java version: > > >> > java version "1.6.0_15" > > >> > Java(TM) SE Runtime Environment (build 1.6.0_15-b03) > > >> > Java HotSpot(TM) Server VM (build 14.1-b02, mixed mode) > > >> > > > >> > Mesquite_log: > > >> > Mesquite version 2.72 (build 527) > > >> > Copyright (c) 1997-2009 W. Maddison and D. Maddison > > >> > The basic Mesquite package (class library and basic modules) is > > >> > free software; you can redistribute it and/or modify it under the > > >> > terms of > > > > the > > > > >> > GNU Lesser General Public License. Mesquite is distributed in the > > > > hope > > > > >> > that it will be useful, but WITHOUT ANY WARRANTY. For details on > > > > license > > > > >> > and lack of warranty see the GNU Lesser General Public License by > > >> > selecting "Display License" from the Window menu or at www.gnu.org > > >> > > > >> > Principal Authors: Wayne Maddison & David Maddison > > >> > Development Team: Wayne Maddison, David Maddison, Peter Midford, > > >> > Jeff Oliver Development Team Alumnus: Danny Mandel > > >> > > > >> > Sat Mar 06 22:11:12 PST 2010 > > >> > Running under Java 1.6.0_15; virtual machine by Sun Microsystems > > >> > Inc. > > > > on > > > > >> > Linux 2.6.31-20-generic (architecture: i386) > > >> > User: gustavo > > >> > > > >> > Incorporated from /home/gustavo/Programs/Mesquite_Folder/./ > > >> > commons- httpclient-3.1.jar Jama-1.0.1.zip JSci.zip pal.zip > > > > commons-codec-1.3.jar > > > > >> > commons-logging-1.1.1.jar dom4j-1.6.1.jar commons-lang-2.3.jar > > > > iText.jar > > > > >> > Mesquite directory: /home/gustavo/Programs/Mesquite_Folder/./ > > >> > Log file located in: /home/gustavo/Mesquite_Support_Files > > >> > Prefs directory: > > >> > /home/gustavo/Mesquite_Support_Files/Mesquite_Prefs > > >> > > > >> > Modules loading from directory > > >> > /home/gustavo/Programs/Mesquite_Folder/./mesquite/ > > >> > > > >> > ancstates basic categ charMatrices charts cont genesis io lists > > > > minimal > > > > >> > parsimony stochchar trees align assoc batchArch coalesce (CRASH!) > > >> > > > >> > > > >> > _______________________________________________ > > >> > Mesquitelist mailing list > > >> > Mesquitelist at mesquiteproject.org > > >> > http://mesquiteproject.org/mailman/listinfo/mesquitelist > > > > > >-- > > >Gustavo Ybazeta > > > > > >Department of Ecology and & Evolutionary Biology > > >University of Toronto > > >Department of Natural History > > >Royal Ontario Museum > > > > > >g.ybazeta"at"utoronto.ca > > >_______________________________________________ > > >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 > > _______________________________________________ > > Mesquitelist mailing list > > Mesquitelist at mesquiteproject.org > > http://mesquiteproject.org/mailman/listinfo/mesquitelist > -- Gustavo Ybazeta Department of Ecology and & Evolutionary Biology University of Toronto Department of Natural History Royal Ontario Museum g.ybazeta"at"utoronto.ca From michel.laurin at upmc.fr Wed Mar 31 01:45:19 2010 From: michel.laurin at upmc.fr (Michel Laurin) Date: Wed, 31 Mar 2010 10:45:19 +0200 Subject: [Mesquitelist] Combining trees with branch lengths information in Mesquite Message-ID: <4BB30B9F.4090105@upmc.fr> Hello all, Does anybody know if it is possible to combine trees in Mesquite while keeping branch length information? I just looked into it and I was unable to find a solution. MRP would not work because it would discard branch lengths. I tried the "Combine trees" or "Condense trees", but these options did not seem to combine or condense anything. What I would like to do is build a large time-calibrated supertree, but give the task to various students, each student having a clade to do. The tree would be compiled using my Stratigraphic Tools to place fossils, but I suppose that this makes no difference in how trees would need to be combined at the end; if branch length information is retained, that would work. I could of course have to put manually the relationships between the combined subtrees, but that is no problem; I envision combining about 3 or 4 source trees. But since entering time information is very time-consuming, I don't want to have to re-enter all branch lengths manually, as I would need to do if I used MRP or something like that. Best wishes, Michel -- Michel Laurin UMR CNRS 7207 Dept. Histoire de la Terre 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 lmandar2 at binghamton.edu Wed Mar 31 18:39:55 2010 From: lmandar2 at binghamton.edu (Lisa Mandarino) Date: Wed, 31 Mar 2010 21:39:55 -0400 Subject: [Mesquitelist] Redundant Taxa Message-ID: Is there a way to merge redundant taxa like in MacClade? Thank you for your help! -Lisa -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100331/e44c682e/attachment.html