From andrevanproosdij at hotmail.com Tue Dec 1 05:28:31 2009 From: andrevanproosdij at hotmail.com (andre vanproosdij) Date: Tue, 1 Dec 2009 13:28:31 +0000 Subject: [Mesquitelist] Tree Set Viz version 3 Message-ID: Hi all, I'm new to Mesquite and would like to use the Tree Set Viz module to calculate Robinson Foulds distances between some trees. However, on the Mesquite page only Tree Set Viz version of 2004 is available which is not compatible to mesquite 2.71. Where can I find version 3 of Tree Set Viz (2009)? If that is not available yet, where can I find older, compatible versions of mesquite? Many thanks in advance for your help. Best wishes, Andr? Ir. A.S.J. van Proosdij Wageningen University The Netherlands _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091201/a81c9c64/attachment.html From wmaddisn at interchange.ubc.ca Tue Dec 1 18:11:07 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Tue, 01 Dec 2009 18:11:07 -0800 Subject: [Mesquitelist] Tree Set Viz version 3 In-Reply-To: References: Message-ID: Our expectation is that Tree Set Viz 3 will be out soon; perhaps the lead authors will comment on when! In the meantime, you can download old versions of Mesquite from the Mesquite home page at http://mesquiteproject.org. At the bottom of the page under Mesquite Chronology there are links to many old versions. Wayne At 1:28 PM +0000 1.12.2009, andre vanproosdij wrote: >Hi all, > >I'm new to Mesquite and would like to use the Tree Set Viz module to >calculate Robinson Foulds distances between some trees. However, on >the Mesquite page only Tree Set Viz version of 2004 is available >which is not compatible to mesquite 2.71. > >Where can I find version 3 of Tree Set Viz (2009)? >If that is not available yet, where can I find older, compatible >versions of mesquite? > >Many thanks in advance for your help. > >Best wishes, > > >Andr? > > > >Ir. A.S.J. van Proosdij >Wageningen University >The Netherlands > > > >New Windows 7: Find the right PC for you. >Learn more. > >_______________________________________________ >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 Dec 20 12:47:03 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 20 Dec 2009 12:47:03 -0800 Subject: [Mesquitelist] Mesquite 2.72 released & bug fixes Message-ID: Mesquite version 2.72 was released on 11 December; due to a glitch in our server, this announcement was delayed. ALL USERS ARE URGED TO UPGRADE because of important bug fixes. Also, after you upgrade and restart Mesquite, you will notice there is a minor update that we also ask you to install to fix a few small bugs. Version 2.72 has improved reporting of crashes and other problems, which means the sooner users upgrade, the better information we will get to continue to improve Mesquite. Download at http://mesquiteproject.org See new features and important bug fixes at http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/changes.html -- ---------------------------------------------------------------------------- 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 josh.brokaw at acu.edu Tue Dec 29 17:12:21 2009 From: josh.brokaw at acu.edu (Joshua M. Brokaw) Date: Tue, 29 Dec 2009 19:12:21 -0600 Subject: [Mesquitelist] acctran/deltran Message-ID: Hi, I would like a confirmation that the parsimony-based, discrete ancestral state reconstructions in Mesquite use acctran optimizations. It would be great if the manual mentioned this in the future also. Thanks, Joshua M. Brokaw, Ph.D. Assistant Professor Department of Biology Abilene Christian University ACU Box 27868 Abilene, Texas 79699-7868 325-674-2168 fax 325-674-2009 josh.brokaw at acu.edu From wmaddisn at interchange.ubc.ca Wed Dec 30 10:41:40 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Wed, 30 Dec 2009 10:41:40 -0800 Subject: [Mesquitelist] acctran/deltran In-Reply-To: References: Message-ID: No, Mesquite does not have the option to use ACCTRAN. By default (as was the case with MacClade) it shows all most parsimonious states at each node. ACCTRAN would attempt to resolve ambiguities in ancestral state reconstructions so as to maximize reversals, although it often can't yield full resolution unless arbitrary choices are made. Mesquite has a method to resolve ambiguities, but instead of choosing one resolution that maximizes reversals, it permits you to see each of the many possible resolutions. This is the MPRs mode. If you need to use ACCTRAN, it's implemented in MacClade. MacClade won't necessarily give a completely resolved reconstruction, however, because that would require (in some cases) arbitrary choices. Wayne At 7:12 PM -0600 29.12.2009, Joshua M. Brokaw wrote: >Hi, > >I would like a confirmation that the parsimony-based, discrete >ancestral state reconstructions in Mesquite use acctran >optimizations. It would be great if the manual mentioned this in the >future also. > >Thanks, > >Joshua M. Brokaw, Ph.D. >Assistant Professor >Department of Biology >Abilene Christian University >ACU Box 27868 >Abilene, Texas 79699-7868 >325-674-2168 >fax 325-674-2009 >josh.brokaw at acu.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