From samd at seas.upenn.edu Thu Nov 5 10:06:45 2009 From: samd at seas.upenn.edu (Sam Donnelly) Date: Thu, 5 Nov 2009 13:06:45 -0500 Subject: [Mesquitelist] CategoricalData.setStateName bug? Message-ID: Hi, It looks to me like there's a bug in mesquite.categ.lib.CategoricalData.setStateName(...) in at least revision 6240 of the trunk: Here's the first couple of lines /** sets state name of state "state" of character ic to name */ public void setStateName(int ic, int state, String name) { //todo: check if in bounds if (ic< 1 || ic >= numChars) return; Should that be "ic < 0" instead of "ic < 1"? Otherwise, it doesn't seem to allow setting state names for the first column of the matrix. thanks! Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091105/dce5c68d/attachment.html From wmaddisn at interchange.ubc.ca Fri Nov 6 08:37:47 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 06 Nov 2009 08:37:47 -0800 Subject: [Mesquitelist] CategoricalData.setStateName bug? In-Reply-To: References: Message-ID: Sam, Yes, a bug -- thanks for noticing it! This is not in any release version, and so won't have affected users. Since MesquiteList is intended primarily for biologists using Mesquite, it's best to put developer discussion of bugs on the MesquiteDev mailing list. Thanks Wayne At 1:06 PM -0500 5.11.2009, Sam Donnelly wrote: >Hi, > >It looks to me like there's a bug >in mesquite.categ.lib.CategoricalData.setStateName(...) in at least >revision 6240 of the trunk: > >Here's the first couple of lines > /** sets state name of state "state" of character ic to name */ > void setStateName(int ic, int state, String name) { //todo: >check if in bounds > if (ic< 1 || ic >= numChars) > return; > > >Should that be "ic < 0" instead of "ic < 1"? Otherwise, it doesn't >seem to allow setting state names for the first column of the >matrix. > >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 v_candida at hotmail.com Sat Nov 14 08:36:12 2009 From: v_candida at hotmail.com (m. candida) Date: Sat, 14 Nov 2009 16:36:12 +0000 Subject: [Mesquitelist] discrepancy in taxa samples Message-ID: I have 8 categorical character states for 134 taxa. The tree I am using (supertree constructed by Bidinda-Edmonds et al, Nature, 2007) has several thousand taxa. Is there a way to use this tree with my data without removing the thousands of irrelevant taxa? I would like to reconstruct ancestral states under parsimony and ML. Any advice would be appreciated. Regards, Therese _________________________________________________________________ Hotmail: Trusted email with Microsoft's powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/ http://clk.atdmt.com/GBL/go/177141664/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091114/55ace2e2/attachment.html From wmaddisn at interchange.ubc.ca Mon Nov 16 09:41:20 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 16 Nov 2009 09:41:20 -0800 Subject: [Mesquitelist] discrepancy in taxa samples In-Reply-To: References: Message-ID: You can reconstruct with missing data, but the results are messy -- you would have to look at thousands of nodes in the tree to find the one you want. Is there a specific reason you don't want to delete the irrelevant taxa? You can quickly delete the irrelevant taxa as follows. Read in the tree & matrix. Go to the matrix editor. Use the magic wand with a T to select all taxa with a ?. Now hit the delete key to delete all taxa with ?. The taxa will be automatically deleted from the tree. Use File>Save as to save the trimmed file. You can delete the irrelevant taxa from the tree (but not the matrix) by selecting all with a ? then going to the tree window and choosing "Cut selected taxa". Does this help? Wayne At 4:36 PM +0000 14.11.2009, m. candida wrote: >I have 8 categorical character states for 134 taxa. The tree I am >using (supertree constructed by Bidinda-Edmonds et al, Nature, 2007) >has several thousand taxa. Is there a way to use this tree with my >data without removing the thousands of irrelevant taxa? I would like >to reconstruct ancestral states under parsimony and ML. Any advice >would be appreciated. > >Regards, >Therese > > >Hotmail: Trusted email with Microsoft's powerful SPAM protection. >http://clk.atdmt.com/GBL/go/177141664/direct/01/ >>Sign up 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 herpgirl at gmail.com Wed Nov 18 10:55:58 2009 From: herpgirl at gmail.com (Allyson Fenwick) Date: Wed, 18 Nov 2009 13:55:58 -0500 Subject: [Mesquitelist] root-fixing for BiSSE? Message-ID: <1c0342480911181055o153a2bb4nb7bf917499659e6d@mail.gmail.com> Wondering if anyone has a script or tips on how to fix a particular node (root or other node) to a single character state in BiSSE, as is needed for a robust test of Dollo's Law. Thanks for the help, Allyson Allyson Fenwick Ph.D. Candidate Department of Biology University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091118/495a1731/attachment.html From biodiverky at gmail.com Fri Nov 20 05:38:44 2009 From: biodiverky at gmail.com (Yi Kong) Date: Fri, 20 Nov 2009 21:38:44 +0800 Subject: [Mesquitelist] A problem in Ancestral State reconstruction. In-Reply-To: <57d1a1d50911200522t5817a3f4w683857874531b286@mail.gmail.com> References: <57d1a1d50911200522t5817a3f4w683857874531b286@mail.gmail.com> Message-ID: <57d1a1d50911200538x8a014b1h21232770ec0f1968@mail.gmail.com> Dear colleague, I intend to employ *Ancestral state reconstruction package *in mesquite in my analysis. However, a fatal problem obstructs my calculations. I import 500 trees from a Bayesian *.t file, then create a character matrix with 35 states, standard category and unorder. Subsequently, I click trace character over tree. Every steps seem normal until I choose "summarize state changes over trees" (Parsimonious model) Clicking this button, calculation begins. When number reaches tree 69, a dialog box jumps out and calculation stops. The warning contents lists below. There has been a problem starting a module (class java.lang.ArithmeticException). (module: Summarize State Changes Over Trees; arguments: null; module being started: null; EXCEPTION: / by zero; exception class class java.lang.ArithmeticException [1]) Please send a report of this crash to the Mesquite server, to help us debug it and improve Mesquite. None of your data will be sent, but your log file up to this point will be sent. It is very strange that I can hardly find what lead to this problem. Would you please give me some advice to deal with this problem? Your assistance is very important to me. Best Wishes! Yours sincerely, Yi Kong -- Yi Kong P.P.BOX 159 No.1 Wenyuan road, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu province 210046, P.R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20091120/3da0c799/attachment.html From wmaddisn at interchange.ubc.ca Fri Nov 20 14:53:52 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 20 Nov 2009 14:53:52 -0800 Subject: [Mesquitelist] A problem in Ancestral State reconstruction. In-Reply-To: <57d1a1d50911200538x8a014b1h21232770ec0f1968@mail.gmail.com> References: <57d1a1d50911200522t5817a3f4w683857874531b286@mail.gmail.com> <57d1a1d50911200538x8a014b1h21232770ec0f1968@mail.gmail.com> Message-ID: This appears to be a problem that we recently fixed for the next version. Would it be possible for you to send me the file (straight to me, not the list) so that we could confirm we understand it? thanks, Wayne At 9:38 PM +0800 20.11.2009, Yi Kong wrote: >Dear colleague, > >I intend to employ Ancestral state reconstruction package in >mesquite in my analysis. However, a fatal problem obstructs my >calculations. > >I import 500 trees from a Bayesian *.t file, then create a character >matrix with 35 states, standard category and unorder. Subsequently, > I click trace character over tree. Every steps seem normal until I >choose "summarize state changes over trees" (Parsimonious model) >Clicking this button, calculation begins. When number reaches tree >69, a dialog box jumps out and calculation stops. The warning >contents lists below. > >There has been a problem starting a module (class >java.lang.ArithmeticException). (module: Summarize State Changes >Over Trees; arguments: null; module being started: null; EXCEPTION: >/ by zero; exception class class java.lang.ArithmeticException [1]) >Please send a report of this crash to the Mesquite server, to help >us debug it and improve Mesquite. None of your data will be sent, >but your log file up to this point will be sent. > > >It is very strange that I can hardly find what lead to this problem. >Would you please give me some advice to deal with this problem? >Your assistance is very important to me. > >Best Wishes! > >Yours sincerely, >Yi Kong > >-- >Yi Kong >P.P.BOX 159 >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 -- -------------------------------------------------------- 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 Nov 29 19:56:00 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 29 Nov 2009 19:56:00 -0800 Subject: [Mesquitelist] root-fixing for BiSSE? In-Reply-To: <1c0342480911181055o153a2bb4nb7bf917499659e6d@mail.gmail.com> References: <1c0342480911181055o153a2bb4nb7bf917499659e6d@mail.gmail.com> Message-ID: The only way to fix the state at a node is by adding a dummy taxon with that state and attaching it to the tree next to the node of interest, and making the connecting branch lengths very very short, effectively forcing the node of interest to have that state. Wayne At 1:55 PM -0500 18.11.2009, Allyson Fenwick wrote: >Wondering if anyone has a script or tips on how to fix a particular >node (root or other node) to a single character state in BiSSE, as >is needed for a robust test of Dollo's Law. > >Thanks for the help, >Allyson > >Allyson Fenwick >Ph.D. Candidate >Department of Biology >University of Central Florida > >_______________________________________________ >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