From kie-bitz at gmx.net Thu Jan 7 03:31:15 2010 From: kie-bitz at gmx.net (Vera Weisbecker) Date: Thu, 7 Jan 2010 11:31:15 -0000 Subject: [Mesquitelist] Very slow Mesquite Message-ID: Dear Mesquitelist, I have a problem running Mesquite on my computer (64 bit, XPx64), latest Java version - it seems to choke on my datasets. When I load a file consisting of a character matrix of 114 species, 12 numeric characters and one tree, the character list takes ages to scroll through, and PDAP plots take extremely long to load. In both cases, the screen is taking a very long time to refresh and sometimes shows just random lines; during that time, I also can't use the mouse or switch to other programs, so the whole computer is slowed down. I tried installing a higher memory version of Mesquite (512 Mb), but that didn't change anything. This problem is not new to the latest version, I have had it previously as well; however, the problem wasn't there when I first got the computer a couple of years ago. Also, it can't be an issue with the XP installation because I recently re-installed it and it the problem didn't go away. I can provide a sample dataset and screenshots. Any help would be much appreciated! Best wishes, Vera Weisbecker Vera Weisbecker Volkswagen Foundation Evolution Initiative Postdoctoral Fellow Earth Sciences Cambridge University Downing Street CB2 3EQ Cambridge UK Phone: +44 1223 768 329 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100107/77decfc7/attachment.html From ligia_oceanica at hotmail.com Thu Jan 7 03:32:40 2010 From: ligia_oceanica at hotmail.com (Ligia Pizzatto do Prado) Date: Thu, 7 Jan 2010 11:32:40 +0000 Subject: [Mesquitelist] Pagel's 94 module Message-ID: Hi there, I'm trying to learn how to use the Pagel's analyses module for correlate evolution of binary characters. I ran the analyses and it gives me a significant p value, but when I look at the ancestral reconstruction it is not obvious what the relationships are. So then I look at q values and compare then. there is only one value that is much higher than all the others (q34), which I compare to the q12 and it's pretty different. That tells me that my Y character is more likely to change from 0 to 1 when X = 1 than when it is 0, right? That's what I understood from Pagel's 1994 paper that describes the method... Anyway, does it mean that the correlation significance relates to this change mainly (cause all other q values are pretty low)... Sorry if this is very basic, I'm trying to learn the method on my own... Cheers Ligia _________________________________________________________________ Agora ? f?cil compartilhar fotos no Messenger: solte todas na janelinha. Veja como! http://www.windowslive.com.br/public/tip.aspx/view/77?product=2&ocid=CRM-WindowsLive:dicaCompartilhamentoFotos:Tagline:WLCRM:On:WL:pt-BR:Messenger -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100107/9049ddbd/attachment.html From samd at seas.upenn.edu Thu Jan 7 07:16:19 2010 From: samd at seas.upenn.edu (Sam Donnelly) Date: Thu, 7 Jan 2010 10:16:19 -0500 Subject: [Mesquitelist] mesquitelist/mesquitedev archive? Message-ID: Hello, Are there archives for the mesquitelist and/or mesquitedev lists anywhere? I've found these: http://mesquiteproject.org/pipermail/mesquitedev/ http://mesquiteproject.org/pipermail/mesquitedev/ but they look to be incomplete. Thanks! Sam From samd at seas.upenn.edu Thu Jan 7 07:35:34 2010 From: samd at seas.upenn.edu (Sam Donnelly) Date: Thu, 7 Jan 2010 10:35:34 -0500 Subject: [Mesquitelist] mesquitelist/mesquitedev archive? In-Reply-To: References: Message-ID: <57595060-1922-41AC-B390-9FC0C51997C3@seas.upenn.edu> One of those links should've read: http://mesquiteproject.org/pipermail/mesquitelist/ On Jan 7, 2010, at 10:16 AM, Sam Donnelly wrote: > Hello, > > Are there archives for the mesquitelist and/or mesquitedev lists anywhere? > > I've found these: > > http://mesquiteproject.org/pipermail/mesquitedev/ > http://mesquiteproject.org/pipermail/mesquitedev/ > > but they look to be incomplete. > > Thanks! > > Sam > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From wmaddisn at interchange.ubc.ca Thu Jan 7 11:27:39 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 07 Jan 2010 11:27:39 -0800 Subject: [Mesquitelist] Very slow Mesquite In-Reply-To: References: Message-ID: Yes, a sample dataset (with exact instructions to reproduce) would be very helpful. thanks, Wayne At 11:31 AM +0000 7.1.2010, Vera Weisbecker wrote: >Dear Mesquitelist, > >I have a problem running Mesquite on my computer (64 bit, XPx64), >latest Java version - it seems to choke on my datasets. When I load >a file consisting of a character matrix of 114 species, 12 numeric >characters and one tree, the character list takes ages to scroll >through, and PDAP plots take extremely long to load. In both cases, >the screen is taking a very long time to refresh and sometimes shows >just random lines; during that time, I also can't use the mouse or >switch to other programs, so the whole computer is >slowed down. I tried installing a higher memory version of Mesquite >(512 Mb), but that didn't change anything. This problem is not new >to the latest version, I have had it previously as well; however, >the problem wasn't there when I first got the computer a couple of >years ago. Also, it can't be an issue with the XP installation >because I recently re-installed it and it the problem didn't go away. > >I can provide a sample dataset and screenshots. Any help would be >much appreciated! > >Best wishes, > > >Vera Weisbecker > > >Vera Weisbecker >Volkswagen Foundation Evolution Initiative Postdoctoral Fellow >Earth Sciences >Cambridge University >Downing Street >CB2 3EQ Cambridge >UK >Phone: +44 1223 768 329 > > >_______________________________________________ >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 Thu Jan 7 11:29:31 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 07 Jan 2010 11:29:31 -0800 Subject: [Mesquitelist] mesquitelist/mesquitedev archive? In-Reply-To: References: Message-ID: There has been a persistent problem with our server in regards to the archives. They are stored in a directory different from what the list webpage points to. Since we have no sysadmin (other than myself) I'd appreciate any volunteers to help fix it. Wayne At 10:16 AM -0500 7.1.2010, Sam Donnelly wrote: >Hello, > >Are there archives for the mesquitelist and/or mesquitedev lists anywhere? > >I've found these: > >http://mesquiteproject.org/pipermail/mesquitedev/ >http://mesquiteproject.org/pipermail/mesquitedev/ > >but they look to be incomplete. > >Thanks! > >Sam >_______________________________________________ >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 samd at seas.upenn.edu Thu Jan 7 11:52:20 2010 From: samd at seas.upenn.edu (Sam Donnelly) Date: Thu, 7 Jan 2010 14:52:20 -0500 Subject: [Mesquitelist] mesquitelist/mesquitedev archive? In-Reply-To: References: Message-ID: <4154F010-81F0-48A7-A65A-868A7A720A50@seas.upenn.edu> Wayne, I'd be happy to help with this. (Assuming that you were't looking for someone who already had login credentials and what-not.) On Jan 7, 2010, at 2:29 PM, Wayne Maddison wrote: > There has been a persistent problem with our server in regards to the archives. They are stored in a directory different from what the list webpage points to. > > Since we have no sysadmin (other than myself) I'd appreciate any volunteers to help fix it. > Wayne > > At 10:16 AM -0500 7.1.2010, Sam Donnelly wrote: >> Hello, >> >> Are there archives for the mesquitelist and/or mesquitedev lists anywhere? >> >> I've found these: >> >> http://mesquiteproject.org/pipermail/mesquitedev/ >> http://mesquiteproject.org/pipermail/mesquitedev/ >> >> but they look to be incomplete. >> >> Thanks! >> >> Sam >> _______________________________________________ >> 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 samd at seas.upenn.edu Thu Jan 7 14:07:17 2010 From: samd at seas.upenn.edu (Sam Donnelly) Date: Thu, 7 Jan 2010 17:07:17 -0500 Subject: [Mesquitelist] supermatrix building Message-ID: <85A901E1-2935-4B5B-9005-CDBB4394D588@seas.upenn.edu> Hello, What tools does Mesquite have for supermatrix building? I've used the Matrix->Utilities->Concatenate Other Matrix tool, but was wondering what else there might be. Other related, but more specific questions: Is there a way to see what characters that two matrices have in common? Is there a way to combine two matrices and join on a column? For example if we had M1 c1 c2 t1 0 1 t2 1 1 M2 c2 c3 t1 1 1 t2 1 0 is there a way to concatenate them to get M1M2 c1 c2 c3 t1 0 1 1 t2 1 1 0 I'm leaving aside the cases where c2 has different states for t1 and t2 in the two matrices. But maybe there's some sort of conflict resolution method for those cases? Thanks! Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100107/9d66ff34/attachment.html From wmaddisn at interchange.ubc.ca Fri Jan 8 08:37:27 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 08 Jan 2010 08:37:27 -0800 Subject: [Mesquitelist] supermatrix building In-Reply-To: <85A901E1-2935-4B5B-9005-CDBB4394D588@seas.upenn.edu> References: <85A901E1-2935-4B5B-9005-CDBB4394D588@seas.upenn.edu> Message-ID: At 5:07 PM -0500 7.1.2010, Sam Donnelly wrote: >Hello, > >What tools does Mesquite have for supermatrix building? I've used >the Matrix->Utilities->Concatenate Other Matrix tool, but was >wondering what else there might be. You can fuse matrices on export to a file using File>Export>Fused Matrix Export (http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/molecular/molecular.html#fusing) > >Other related, but more specific questions: > >Is there a way to see what characters that two matrices have in common? The answer would always be "none" -- there is no sense of a character existing in more than one matrix at once. This would be possible if we treated character names as full-blown identifiers (which we don't) or if characters in different matrices would share the same unique ID (which they don't in practice). If we were to support such cross-matrix characters, we'd have to ensure their editing was synchronized (changes in one matrix immediately showed up in the other) and we'd have to design an interface to make it clear that these columns were linked. It wouldn't make sense to let these characters differ ever; they would simply be two views into the same data. Because of this we don't do any automatic column joining. We could have a merge character feature that merges states of columns (regardless of whether the characters started off as the same) but we don't have such. Wayne > >Is there a way to combine two matrices and join on a column? For >example if we had > >M1 > c1 c2 >t1 0 1 >t2 1 1 > >M2 > c2 c3 >t1 1 1 >t2 1 0 > >is there a way to concatenate them to get > >M1M2 > c1 c2 c3 >t1 0 1 1 >t2 1 1 0 > >I'm leaving aside the cases where c2 has different states for t1 and >t2 in the two matrices. But maybe there's some sort of conflict >resolution method for those cases? > >Thanks! > >Sam > > >_______________________________________________ >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 Tue Jan 12 11:41:48 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Tue, 12 Jan 2010 11:41:48 -0800 Subject: [Mesquitelist] R - Mesquite communication package In-Reply-To: <28446_1262968668_1262968668_a06240820c76d0c19a14a@[192.168.0.182]> References: <85A901E1-2935-4B5B-9005-CDBB4394D588@seas.upenn.edu> <28446_1262968668_1262968668_a06240820c76d0c19a14a@[192.168.0.182]> Message-ID: We'd like to announce the beta release of packages for communication between Mesquite and R. Mesquite is a graphical application for phylogenetic and evolutionary analysis; R is a system for statistical computation primarily oriented around text-based programming. We have enabled communication in both directions: -- Mesquite.R enables Mesquite to make use of functions in R (http://mesquiteproject.org/packages/mesquite.R/MesquiteCallsR/MesquiteR.html). At the moment these include functions in the R packages ape and diversitree. -- RMesquite enables R programs to make use of Mesquite, either as a graphical interface for editing trees and data, or to provide its broad array of phylogenetic calculations to R. (http://rmesquite.r-forge.r-project.org) Only a handful of functions have been enabled in each direction; we seek your input as to what functions would be of most interest to R users and Mesquite users. You may consider this as an experimental release for thrill-seekers. Please tell us if something doesn't seem to work or is confusing -- feedback is much appreciated. We hope to continue to strengthen the links between R and Mesquite. Wayne & Hilmar Wayne Maddison, UBC Hilmar Lapp, Duke From dclarke at fieldmuseum.org Fri Jan 15 21:38:19 2010 From: dclarke at fieldmuseum.org (Dave Clarke) Date: Fri, 15 Jan 2010 23:38:19 -0600 Subject: [Mesquitelist] Mesquite-NDE-DELTA compatibility Message-ID: <1ce927da1001152138x1fcdde37j3778c47d35b59e8f@mail.gmail.com> Hello, I have a morphological matrix in Mesquite that I would like to open in Nexus Data Editor but it will only open when I manually remove everything from the nexus file except the taxa and characters blocks (suppressing the TITLES block doesn't help). The problem is that while it reads the matrix fine the resulting file in NDE lacks all character and state names (i.e., they're "Untitled"). If someone can help me out with this I'd be most grateful. I'm ultimately trying to get the matrix into the DELTA system (NDE can export to DELTA format) - is this actually possible to do directly from Mesquite? Best regards, Dave -- Dave J. Clarke PhD Candidate Zoology Department, Division of Insects The Field Museum 1400 S Lake Shore Drive Chicago IL 60605 USA +1-312-665-7014 +1-773-573-2000 University of Illinois at Chicago 845 W. Taylor St. M/C 066 Chicago, IL 60607 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100115/5fe126e3/attachment.html From wmaddisn at interchange.ubc.ca Fri Jan 15 22:18:36 2010 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 15 Jan 2010 22:18:36 -0800 Subject: [Mesquitelist] Mesquite-NDE-DELTA compatibility In-Reply-To: <1ce927da1001152138x1fcdde37j3778c47d35b59e8f@mail.gmail.com> References: <1ce927da1001152138x1fcdde37j3778c47d35b59e8f@mail.gmail.com> Message-ID: There are two ways in NEXUS to indicate character and state names, CharStateLabels versus CharLabels+StateLabels. The paper describing the NEXUS standard recommended against the latter. Mesquite can read either but writes only the CharStateLabels. Perhaps NDE can read only CharLabels and StateLabels? We will explore the possibility of writing CharLabels and StateLabels when File>Export>Simplified NEXUS is chosen (thus treating it as "simplified and archaic NEXUS"). Wayne At 11:38 PM -0600 15.1.2010, Dave Clarke wrote: >Hello, > >I have a morphological matrix in Mesquite that I would like to open >in Nexus Data Editor but it will only open when I manually remove >everything from the nexus file except the taxa and characters blocks >(suppressing the TITLES block doesn't help). The problem is that >while it reads the matrix fine the resulting file in NDE lacks all >character and state names (i.e., they're "Untitled"). If someone can >help me out with this I'd be most grateful. > >I'm ultimately trying to get the matrix into the DELTA system (NDE >can export to DELTA format) - is this actually possible to do >directly from Mesquite? > >Best regards, > >Dave > > >-- >Dave J. Clarke >PhD Candidate >Zoology Department, Division of Insects >The Field Museum >1400 S Lake Shore Drive >Chicago IL 60605 >USA >+1-312-665-7014 >+1-773-573-2000 > >University of Illinois at Chicago >845 W. Taylor St. M/C 066 >Chicago, IL 60607 > >_______________________________________________ >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 travis at traviswheeler.com Tue Jan 26 18:48:32 2010 From: travis at traviswheeler.com (Travis Wheeler) Date: Tue, 26 Jan 2010 21:48:32 -0500 Subject: [Mesquitelist] Announcing new neighbor-joining package (NINJA) Message-ID: Hello Mesquite users, I'm pleased to announce the release of a new Mesquite package that brings a fast neighbor-joining algorithm (NINJA, http://nimbletwist.com/software/ninja/) into the Mesquite toolkit. To install the NINJA package of modules, start up Mesquite. Then use the "Check Now for Notices/Installs" menu item in the File Menu, and enter the URL http://mesquiteproject.org/packages/NINJA/install.xml Mesquite will then present a dialog box with information, and from which you can install NINJA. Best, Travis Wheeler From david.maddison at science.oregonstate.edu Wed Jan 27 09:22:56 2010 From: david.maddison at science.oregonstate.edu (David Maddison) Date: Wed, 27 Jan 2010 09:22:56 -0800 Subject: [Mesquitelist] Announcing new neighbor-joining package (NINJA) In-Reply-To: References: Message-ID: As a follow-up to Travis's note about NINJA: in bringing NINJA to Mesquite, Travis and I realized that NINJA's speed was not matched by a similarly fast distance calculator in Mesquite. That is, while NINJA is very fast, Mesquite's distance calculations aren't. While I have improved the distance calculations by about 2x for the yet-to-be-released version 2.73 of Mesquite, they are still relatively slow. We will work on that in the future. Also, models for calculating distances do not include the full set available in other programs. For example, Mesquite can calculate F84 distances (similar to HKY85), but cannot yet calculate distances using a GTR model. Those, too, we hope to improve. In the meantime, NINJA now brings a fast NJ calculator for the distance measures Mesquite does support. [BTW, once NINJA is installed, you can calculate a neighbor-joining tree using Taxa&Trees > Tree Inference > Neighbor-Joining (NINJA).] David --------------------------------- David R. Maddison Department of Zoology 3029 Cordley Hall Oregon State University Corvallis, OR 97331 USA david.maddison at science.oregonstate.edu http://david.bembidion.org http://mesquiteproject.org http://macclade.org http://tolweb.org (541) 737 2834