From wmaddisn at interchange.ubc.ca Mon Sep 7 12:29:47 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 07 Sep 2009 12:29:47 -0700 Subject: [Mesquitelist] Mesquite 2.71 released Message-ID: We've released a minor update to Mesquite, version 2.71. If you have version 2.7, you won't need to download a whole copy. Rather, just start Mesquite (while connected to the internet) and you'll get a notice; hit "install" and Mesquite will self-update. Otherwise, you can download a whole copy of 2.71 at http://mesquiteproject.org/mesquite/download/download.html There are a few bug fixes in 2.71, none of which are substantive. The primary new features involve the error reporting system that helps us find and fix bugs. We suggest you upgrade, especially since the procedure is quick for users of 2.7. If you're still using a version prior to 2.7, then please update to the latest version. There were several important bug fixes between version 2.6 and 2.7 (see http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/changes.html). -- ------------------------------------------------------------------- Wayne Maddison David R. Maddison Departments of Zoology and Botany Department of Entomology University of British Columbia University of Arizona Vancouver, BC V6T 1Z4 Tucson, AZ 85721 email: wmaddisn at interchange.ubc.ca email: beetle at ag.arizona.edu Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Tree of Life: http://tolweb.org From kirchoff at uncg.edu Mon Sep 7 12:40:52 2009 From: kirchoff at uncg.edu (Bruce Kirchoff KIRCHOFF) Date: Mon, 7 Sep 2009 15:40:52 -0400 Subject: [Mesquitelist] Trace over trees Message-ID: I am having display problems with trace over trees. I am using discrete character data and parsimony. The matrix came from a colleague, from a 2003 publication. I am adding characters are trying to reconstruct their history on the published tree. These problems have not occurred on Mesquite files that I started myself. Problems 1) When I click on a color in a label nothing happens. I should be able to change the character display color on the tree. 2) When I uncheck Use Gray for Equivocal, the tree display remains the same. Equivocal states remain gray, not half white/half black as I need them to be for consistency with other figures. 3) The states of the terminal taxa are displayed in the following way: gray box = ?; no box (white) = 0; black box = 1. I would like the missing data to be no box (white = invisible), and 0 and 1 to be some shade of gray/black. Any help you can provide would be greatly appreciated. I am running 2.7 and had a crash today when I tried an illegal (for this type of data) operation. The reporting routine seemed to hang, so I canceled it. Best wishes, Bruce -------------------- Dr. Bruce K. Kirchoff UNCG, Department of Biology P.O. Box 26170 312 Eberhart, 321 McIver St. Greensboro, NC 27402-6170, USA Voice: 336-334-4953 Fax: 336-334-5839 Home Page: http://www.uncg.edu/~kirchoff/ Save the Earth: http://green-biology.blogspot.com/ From wmaddisn at interchange.ubc.ca Mon Sep 7 14:23:41 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 07 Sep 2009 14:23:41 -0700 Subject: [Mesquitelist] Trace over trees In-Reply-To: References: Message-ID: At 3:40 PM -0400 7.9.2009, Bruce Kirchoff KIRCHOFF wrote: >I am having display problems with trace over trees. I am using discrete >character data and parsimony. The matrix came from a colleague, from a 2003 >publication. I am adding characters are trying to reconstruct their history >on the published tree. These problems have not occurred on Mesquite files >that I started myself. > >Problems > >1) When I click on a color in a label nothing happens. I should be able to >change the character display color on the tree. That feature is available in Trace Character History. It is not yet available in Trace Character over Trees. > >2) When I uncheck Use Gray for Equivocal, the tree display remains the >same. Equivocal states remain gray, not half white/half black as I need >them to be for consistency with other figures. Sorry, that menu item should not appear in the context of Trace Character over Trees. We will fix this. (It appears because we are using the same colouring module for both TCoT and Trace Character History -- it turns out that internally the toggle still makes sense, but to the user it makes no sense.) The reason we don't let you show equivocal directly by multiple colours is that for Trace Character Over Trees there are complex possibilities that are hard to summarize. For example, how to differentiate graphically these cases?: (1) 5 trees with state 0, 5 trees with 1, 5 trees with 2 (2) 10 trees with 0,1 and 5 with state 2 (3) 5 trees with state 0, 10 with state 1,2. (4) 5 trees with state 0,1; 5 trees with state 0,2; 5 trees with state 1,2. And so on. > >3) The states of the terminal taxa are displayed in the following way: gray >box = ?; no box (white) = 0; black box = 1. I would like the missing data >to be no box (white = invisible), and 0 and 1 to be some shade of >gray/black. OK, we will see how hard this would be to arrange. In the meantime, you can delete the boxes in the output pdf using Illustrator or other such program. > >Any help you can provide would be greatly appreciated. > >I am running 2.7 and had a crash today when I tried an illegal (for this >type of data) operation. The reporting routine seemed to hang, so I >canceled it. Is there a way we could get a data file from you and instructions as to how to reproduce this? Thanks, Wayne -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn at interchange.ubc.ca FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html From alexandre.antonelli at systbot.uzh.ch Wed Sep 9 05:20:45 2009 From: alexandre.antonelli at systbot.uzh.ch (Alexandre Antonelli) Date: Wed, 9 Sep 2009 14:20:45 +0200 Subject: [Mesquitelist] communication between R and Mesquite Message-ID: Dear all, I recently saw that in the end of March this year (30/03/09), Wayne wrote about the possibility of communicating between R and Mesquite. I wonder whether anything has been implemented yet? More especifically, I would like to pull out the results from parsimony optimizations over discrete values in Mesquite, and than translate the node numbers in Mesquite to those in R (as used by the ape package). For my purposes I would need some way of capturing the output of each tree optimization in Mesquite across a tree sample (rather than computing relative proportions of states at nodes of a reference tree), and for each tree get a translation table specifying how nodes would be numbered in R. Does anyone have scripts for any of these purposes, or any suggestions? Thank you very much in advance! Best wishes, Alex Dr Alexandre Antonelli Institute of Systematic Botany Zollikerstrasse 107 CH 8008 Z?rich Switzerland Phone: +41 (0)44 634 8416 Mobile: + 41 (0) 76 7345116 alexandre.antonelli at systbot.uzh.ch http://www.systbot.uzh.ch/Personen/PostdoktorandInnen/AlexandreAntonelli.html ****************************************************** ON-LINE SURVEY (~5 min.) Have you ever considered doing research in Brazil? http://www.systbot.uzh.ch/brazil/questionnaire_form.php ****************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090909/a7a1431a/attachment.html From ramirez at macn.gov.ar Wed Sep 9 06:26:21 2009 From: ramirez at macn.gov.ar (Martin Ramirez) Date: Wed, 09 Sep 2009 10:26:21 -0300 Subject: [Mesquitelist] communication between R and Mesquite In-Reply-To: References: Message-ID: <20090909132508.8A9F41C5693@ms.macn.gov.ar> Hello Alex, If you are in a hurry, you can write a TNT script yourself to do this (http://tnt.insectmuseum.org). The values can be outputted to a text file. I usually make my scripts to write comma delimited files (.csv), which will open in Excel readily separated in columns. From that to R should be easy. I suggest exploring the following scripting commands: ITERRECS states [ C N T ] Best wishes, Martin At 09:20 AM 9/9/2009, you wrote: >Dear all, > > I recently saw that in the end of March this > year (30/03/09), Wayne wrote about the > possibility of communicating between R and > Mesquite. I wonder whether anything has been implemented yet? > > More especifically, I would like to pull out > the results from parsimony optimizations over > discrete values in Mesquite, and than translate > the node numbers in Mesquite to those in R (as > used by the ape package). For my purposes I > would need some way of capturing the output of > each tree optimization in Mesquite across a > tree sample (rather than computing relative > proportions of states at nodes of a reference > tree), and for each tree get a translation > table specifying how nodes would be numbered in R. > > Does anyone have scripts for any of these purposes, or any suggestions? > >Thank you very much in advance! > >Best wishes, > >Alex > >Dr Alexandre Antonelli >Institute of Systematic Botany >Zollikerstrasse 107 >CH 8008 Z?rich >Switzerland >Phone: +41 (0)44 634 8416 >Mobile: + 41 (0) 76 7345116 >alexandre.antonelli at systbot.uzh.ch >http://www.systbot.uzh.ch/Personen/PostdoktorandInnen/AlexandreAntonelli.html >****************************************************** >ON-LINE SURVEY (~5 min.) >Have you ever considered doing research in Brazil? >http://www.systbot.uzh.ch/brazil/questionnaire_form.php >****************************************************** > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist Martin J. Ramirez Curador General & Divisi?n Aracnolog?a Museo Argentino de Ciencias Naturales - CONICET Av. Angel Gallardo 470 C1405DJR Buenos Aires Argentina tel +54 11 4982-8370 int. 169 fax +54 11 4982-4494 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090909/483e8dce/attachment.html From CATFISH at MAIL.UTEXAS.EDU Sun Sep 13 16:55:52 2009 From: CATFISH at MAIL.UTEXAS.EDU (David Cannatella) Date: Sun, 13 Sep 2009 18:55:52 -0500 Subject: [Mesquitelist] Possible problem with Mesquite 2.71 Message-ID: <39DB6A4C-E6D0-4711-9ACB-63BD8E005B50@MAIL.UTEXAS.EDU> David and Wayne, I had a potentially serious problem with Mesquite today (2.71); unfortunately I can't totally reconstruct the sequence of events. Here is what I can reconstruct: I was using 2.7 (had not yet upgraded to 2.71). I loaded a file that included two character blocks (12S and RAG1) and their taxon blocks. The file also included a third taxon block that was used to associate the 12S and RAG1 taxon blocks. The file loaded with no problem. I can't remember the sequence of the next two events, but I did them one after the other. A. I renamed the RAG1 taxon block, but not the character block. B. I upgraded 2.7 to 2.71. I then quit and re-started to load 2.71. The file doesn't load properly. Specifically it says that can't match the RAG1 character block with its taxon block. It keeps the RAG1 taxon block, but treats the character block as "foreign", and the character block does not show up in the listing of character blocks. The third, association taxon block also does not show up in Mesquite. Upon saving the file, the character matrix and association block are lost. Unfortunately, I don't have a copy of the file as it was before I started this work today, so I can't re-create the error. However, I can send you (David or Wayne) the saved file, which still generates the error that it can't match the RAG1 character block with its taxon block. I have attached the three log files from today. Let me know if you want the datafiles. Dave -------------- next part -------------- A non-text attachment was scrubbed... Name: Mesquite_Log_(Previous#3) Type: application/octet-stream Size: 9848 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090913/531000c9/attachment-0003.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Mesquite_Log_(Previous#2) Type: application/octet-stream Size: 18650 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090913/531000c9/attachment-0004.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: Mesquite_Log_(Previous#1) Type: application/octet-stream Size: 35296 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090913/531000c9/attachment-0005.obj -------------- next part -------------- David Cannatella 512-471-5302 (lab) Professor, Integrative Biology 512-232-4862 (office; voicemail) 1 University Station C0930 512-471-3878 (fax) University of Texas Austin, Texas 78712 www.cannatellalab.org Curator of Herpetology, Texas Natural Science Center From wmaddisn at interchange.ubc.ca Sun Sep 13 22:05:24 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 13 Sep 2009 22:05:24 -0700 Subject: [Mesquitelist] communication between R and Mesquite In-Reply-To: References: Message-ID: It's easy to get the ancestral state reconstructions output to a line in a text file, and repeat for many trees. The difficult part is the translation table for ape node numbering. The Mesquite-R communication isn't quite ready yet. Would you need the tree with its ancestral states specified in R commands for ape? Mart?n's answer may help you, as long as TNT is able to write out trees & ancestral states in ape format. It would be useful for us to have from you some small examples of exactly what you would like Mesquite to output. If you want to send them to us off-list, we can see whether it's easy to include this among the features of the Mesquite-R communication system. Wayne At 2:20 PM +0200 9.9.2009, Alexandre Antonelli wrote: >Dear all, > > I recently saw that in the end of March this year (30/03/09), >Wayne wrote about the possibility of communicating between R and >Mesquite. I wonder whether anything has been implemented yet? > > More especifically, I would like to pull out the results from >parsimony optimizations over discrete values in Mesquite, and than >translate the node numbers in Mesquite to those in R (as used by the >ape package). For my purposes I would need some way of capturing the >output of each tree optimization in Mesquite across a tree sample >(rather than computing relative proportions of states at nodes of a >reference tree), and for each tree get a translation table >specifying how nodes would be numbered in R. > > Does anyone have scripts for any of these purposes, or any suggestions? > >Thank you very much in advance! > >Best wishes, > >Alex > >Dr Alexandre Antonelli >Institute of Systematic Botany >Zollikerstrasse 107 >CH 8008 Z?rich >Switzerland >Phone: +41 (0)44 634 8416 >Mobile: + 41 (0) 76 7345116 >alexandre.antonelli at systbot.uzh.ch >http://www.systbot.uzh.ch/Personen/PostdoktorandInnen/AlexandreAntonelli.html >****************************************************** >ON-LINE SURVEY (~5 min.) >Have you ever considered doing research in Brazil? >http://www.systbot.uzh.ch/brazil/questionnaire_form.php >****************************************************** > > >_______________________________________________ >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 Mon Sep 14 09:17:22 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 14 Sep 2009 09:17:22 -0700 Subject: [Mesquitelist] taxa block names with underscore etc. In-Reply-To: <39DB6A4C-E6D0-4711-9ACB-63BD8E005B50@MAIL.UTEXAS.EDU> References: <39DB6A4C-E6D0-4711-9ACB-63BD8E005B50@MAIL.UTEXAS.EDU> Message-ID: David's problem reflects a bug that reveals itself when a file has more than one taxa block, more than one matrix, and the name of a taxa block includes certain characters such as underscore (David's 'Taxa_RAG1'). In this situation Mesquite has a trouble matching character matrices to taxa blocks. We'll have this fixed for the next update, but in the meantime avoid underscores and punctuation in taxa block names if your files have multiple taxa blocks. This bug goes way way back (back to Mesquite 1.0 probably), and so if it hasn't affected you yet, don't worry too much about it. Wayne At 6:55 PM -0500 13.9.2009, David Cannatella wrote: >David and Wayne, > >I had a potentially serious problem with Mesquite today (2.71); >unfortunately I can't totally reconstruct the sequence of events. > >Here is what I can reconstruct: > >I was using 2.7 (had not yet upgraded to 2.71). I loaded a file >that included two character blocks (12S and RAG1) and their taxon >blocks. >The file also included a third taxon block that was used to >associate the 12S and RAG1 taxon blocks. The file loaded with no >problem. > >I can't remember the sequence of the next two events, but I did them >one after the other. >A. I renamed the RAG1 taxon block, but not the character block. >B. I upgraded 2.7 to 2.71. > >I then quit and re-started to load 2.71. > >The file doesn't load properly. Specifically it says that can't >match the RAG1 character block with its taxon block. It keeps the >RAG1 taxon block, but treats the character block as "foreign", and >the character block does not show up in the listing of character >blocks. > >The third, association taxon block also does not show up in Mesquite. >Upon saving the file, the character matrix and association block are lost. > > >Unfortunately, I don't have a copy of the file as it was before I >started this work today, so I can't re-create the error. However, I >can send you (David or Wayne) the saved file, which still generates >the error that it can't match the RAG1 character block with its >taxon block. > >I have attached the three log files from today. Let me know if you >want the datafiles. > >Dave > > >Attachment converted: Thrandina:Mesquite_Log_(Previous#3) 15 >(TEXT/R*ch) (00435F22) >Attachment converted: Thrandina:Mesquite_Log_(Previous#2) 21 >(TEXT/R*ch) (00435F23) >Attachment converted: Thrandina:Mesquite_Log_(Previous#1) 45 >(TEXT/R*ch) (00435F24) > > > >David Cannatella 512-471-5302 (lab) >Professor, Integrative Biology 512-232-4862 (office; >voicemail) >1 University Station C0930 512-471-3878 (fax) >University of Texas >Austin, Texas 78712 >www.cannatellalab.org >Curator of Herpetology, Texas Natural Science Center > > > > >_______________________________________________ >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 hlapp at duke.edu Wed Sep 16 12:23:55 2009 From: hlapp at duke.edu (Hilmar Lapp) Date: Wed, 16 Sep 2009 15:23:55 -0400 Subject: [Mesquitelist] communication between R and Mesquite In-Reply-To: References: Message-ID: Hi Alexandre, the 2007 Comparative Methods in R hackathon [1] resulted, among many other things, in a package called R/Mesquite [2], with the principle goal to allow you to call into Mesquite from within R, pretending that you are calling "normal" R functions. The code worked the last time I tested it with Mesquite 2.6 and R 2.7. But there also is no installation or usage documentation that deserves that name even remotely, and the calling into Mesquite isn't generic yet, and so the method you're interested in likely isn't among the few we've mapped so far. The code does show though how you do the conversion to an ape (class "phylo") tree, so maybe it's not completely useless to you. And if you come up with any code that bridges between R and Mesquite I'd be very interested. -hilmar [1] http://hackathon.nescent.org/R_Hackathon_1 [2] https://www.nescent.org/wg/phyloinformatics/index.php?title=R_Hackathon_1 On Sep 14, 2009, at 1:05 AM, Wayne Maddison wrote: > It's easy to get the ancestral state reconstructions output to a line > in a text file, and repeat for many trees. The difficult part is the > translation table for ape node numbering. > > The Mesquite-R communication isn't quite ready yet. Would you need > the tree with its ancestral states specified in R commands for ape? > Mart?n's answer may help you, as long as TNT is able to write out > trees & ancestral states in ape format. > > It would be useful for us to have from you some small examples of > exactly what you would like Mesquite to output. If you want to send > them to us off-list, we can see whether it's easy to include this > among the features of the Mesquite-R communication system. > > Wayne > > > > > At 2:20 PM +0200 9.9.2009, Alexandre Antonelli wrote: >> Dear all, >> >> I recently saw that in the end of March this year (30/03/09), >> Wayne wrote about the possibility of communicating between R and >> Mesquite. I wonder whether anything has been implemented yet? >> >> More especifically, I would like to pull out the results from >> parsimony optimizations over discrete values in Mesquite, and than >> translate the node numbers in Mesquite to those in R (as used by the >> ape package). For my purposes I would need some way of capturing the >> output of each tree optimization in Mesquite across a tree sample >> (rather than computing relative proportions of states at nodes of a >> reference tree), and for each tree get a translation table >> specifying how nodes would be numbered in R. >> >> Does anyone have scripts for any of these purposes, or any >> suggestions? >> >> Thank you very much in advance! >> >> Best wishes, >> >> Alex >> >> Dr Alexandre Antonelli >> Institute of Systematic Botany >> Zollikerstrasse 107 >> CH 8008 Z?rich >> Switzerland >> Phone: +41 (0)44 634 8416 >> Mobile: + 41 (0) 76 7345116 >> alexandre.antonelli at systbot.uzh.ch >> > >http://www.systbot.uzh.ch/Personen/PostdoktorandInnen/AlexandreAntonelli.html >> ****************************************************** >> ON-LINE SURVEY (~5 min.) >> Have you ever considered doing research in Brazil? >> http://www.systbot.uzh.ch/brazil/questionnaire_form.php >> ****************************************************** >> >> >> _______________________________________________ >> 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : =========================================================== From hlapp at duke.edu Thu Sep 17 07:45:11 2009 From: hlapp at duke.edu (Hilmar Lapp) Date: Thu, 17 Sep 2009 10:45:11 -0400 Subject: [Mesquitelist] communication between R and Mesquite In-Reply-To: References: Message-ID: On Sep 16, 2009, at 3:23 PM, Hilmar Lapp wrote: > the 2007 Comparative Methods in R hackathon [1] resulted, among many > other things, in a package called R/Mesquite [2], with the principle > goal to allow you to call into Mesquite from within R, pretending that > you are calling "normal" R functions. It turns out I gave the wrong URL for [2]. Sorry 'bout that. Here's the correct one for the archives (I sent to Alex before already): http://r-forge.r-project.org/projects/rmesquite/ -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : =========================================================== From wollenbergk at niaid.nih.gov Tue Sep 22 07:49:24 2009 From: wollenbergk at niaid.nih.gov (Wollenberg, Kurt (NIH/NIAID) [C]) Date: Tue, 22 Sep 2009 10:49:24 -0400 Subject: [Mesquitelist] Underscores in taxon names (again) Message-ID: Hello all: I had an error pop up in a recent Mesquite 2.71 session that appears to be related to the recently publicized problem with underscores in taxon names. In my case I was attempting to import a tree to go with an imported character matrix. I got the error message "Unrecognized name ("A 123") of terminal taxon in tree." The taxon name in the character matrix (and original fasta file) was A_123. The tree ends up not being imported, though I can infer a tree from the character matrix. As I am trying to map character changes on a specific tree this is rate-limiting step to my analysis. Is there a safe character I can replace my underscores with so the tree will be imported? Cheers, Kurt Wollenberg, Ph.D. Contractor, Lockheed Martin Phylogenetics Specialist Biocomputing Research Consulting Section Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62 Bethesda, MD 20892-0485 http://bioinformatics.niaid.nih.gov Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From jschulte at clarkson.edu Wed Sep 23 21:07:57 2009 From: jschulte at clarkson.edu (James Schulte) Date: Thu, 24 Sep 2009 00:07:57 -0400 Subject: [Mesquitelist] bug in rarefy tree? In-Reply-To: References: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu> Message-ID: Dear Wayne, I may have found a bug in version 2.71 regarding rarefying trees. I am trying to do some analyses where I highlight a clade and would like to randomly remove XX number of taxa from that selected clade. I am able to do this in version 2.6 build 486 but when I use the same data set and tree in v. 2.71 it does not work. I am attaching the rarefytree class from 2.6 if you want to compare to 2.71. Do you want the dataset I tried too? Is this a bug in 2.71, you think? Thank you very much for your help. Best, Jim -------------- next part -------------- A non-text attachment was scrubbed... Name: RarefyTree.class Type: application/octet-stream Size: 3790 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090924/28fafe7b/attachment.class -------------- next part -------------- James A. Schulte, II Department of Biology 177 Clarkson Science Center, MRC 5805 8 Clarkson Avenue Clarkson University Potsdam, NY 13699-5805 Phone: 315-268-4401 Fax: 315-268-7118 From jschulte at clarkson.edu Thu Sep 24 06:19:48 2009 From: jschulte at clarkson.edu (James Schulte) Date: Thu, 24 Sep 2009 09:19:48 -0400 Subject: [Mesquitelist] bug in rarefy tree? In-Reply-To: References: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu> Message-ID: <3ABA5209-DAE2-4318-B485-A7E2E74AEC11@clarkson.edu> Dear Wayne, I may have found a bug in version 2.71 regarding rarefying trees. I am trying to do some analyses where I highlight a clade and would like to randomly remove XX number of taxa from that selected clade. I am able to do this in version 2.6 build 486 but when I use the same data set and tree in v. 2.71 it does not work. Is this a bug in 2.71, you think? Thank you very much for your help. However, now it will not let me do it in version 2.6 after leaving it along for a few hours. I appreciate any help. Best, Jim James A. Schulte, II Department of Biology 177 Clarkson Science Center, MRC 5805 8 Clarkson Avenue Clarkson University Potsdam, NY 13699-5805 Phone: 315-268-4401 Fax: 315-268-7118 _______________________________________________ Mesquitelist mailing list Mesquitelist at mesquiteproject.org http://mesquiteproject.org/mailman/listinfo/mesquitelist From wmaddisn at interchange.ubc.ca Sat Sep 26 19:04:19 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sat, 26 Sep 2009 19:04:19 -0700 Subject: [Mesquitelist] Underscores in taxon names (again) In-Reply-To: References: Message-ID: Thanks for the report. The recently publicized problem concerned names of whole taxa blocks, not the names of individual taxa. So, either you've found a new problem in Mesquite, or there is an error in your files. I just tried to import trees with underscores but everything worked. It could be that the issue arises only in some special context. Could you send me off-list the two files (the file with matrix and the file with trees) so that I could diagnose? Thanks, Wayne At 10:49 AM -0400 22.9.2009, Wollenberg, Kurt (NIH/NIAID) [C] wrote: >Hello all: > >I had an error pop up in a recent Mesquite 2.71 session that appears to be >related to the recently publicized problem with underscores in taxon names. >In my case I was attempting to import a tree to go with an imported >character matrix. I got the error message "Unrecognized name ("A 123") of >terminal taxon in tree." The taxon name in the character matrix (and >original fasta file) was A_123. The tree ends up not being imported, though >I can infer a tree from the character matrix. As I am trying to map >character changes on a specific tree this is rate-limiting step to my >analysis. Is there a safe character I can replace my underscores with so the >tree will be imported? > >Cheers, >Kurt Wollenberg, Ph.D. >Contractor, Lockheed Martin >Phylogenetics Specialist >Biocomputing Research Consulting Section >Bioinformatics and Computational Biosciences Branch (BCBB) >OCICB/OSMO/OD/NIAID/NIH > >31 Center Drive, Room 3B62 >Bethesda, MD 20892-0485 >http://bioinformatics.niaid.nih.gov > >Disclaimer: >The information in this e-mail and any of its attachments is confidential >and may contain sensitive information. It should not be used by anyone who >is not the original intended recipient. If you have received this e-mail in >error please inform the sender and delete it from your mailbox or any other >storage devices. National Institute of Allergy and Infectious Diseases shall >not accept liability for any statements made that are sender's own and not >expressly made on behalf of the NIAID by one of its representatives. > > >_______________________________________________ >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 Sep 27 20:57:30 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 27 Sep 2009 20:57:30 -0700 Subject: [Mesquitelist] bug in rarefy tree? In-Reply-To: <3ABA5209-DAE2-4318-B485-A7E2E74AEC11@clarkson.edu> References: <85E05E65-A3AD-4612-9245-0C2282E6B7AC@clarkson.edu> <3ABA5209-DAE2-4318-B485-A7E2E74AEC11@clarkson.edu> Message-ID: Rarefy Tree seems to be working well in my tests, but perhaps you've found a special circumstance. When you say that it doesn't work, what do you mean? It crashes? Nothing happens? It rarefies the tree but not as you expect it? It does something other than rarefying the tree? Do you have the terminal taxa in the clade highlighted (correct) or the clade's branches highlighted (incorrect)? If you could send a data file that consistently shows the incorrect behaviour, with step by step instructions to make it happen, it would be helpful. Thanks, Wayne At 9:19 AM -0400 24.9.2009, James Schulte wrote: >Dear Wayne, > >I may have found a bug in version 2.71 regarding rarefying trees. I >am trying to do some analyses where I highlight a clade and would >like to randomly remove XX number of taxa from that selected clade. >I am able to do this in version 2.6 build 486 but when I use the same >data set and tree in v. 2.71 it does not work. > > >Is this a bug in 2.71, you think? > >Thank you very much for your help. > >However, now it will not let me do it in version 2.6 after leaving it >along for a few hours. I appreciate any help. > >Best, >Jim > > >James A. Schulte, II >Department of Biology >177 Clarkson Science Center, MRC 5805 >8 Clarkson Avenue >Clarkson University >Potsdam, NY 13699-5805 >Phone: 315-268-4401 >Fax: 315-268-7118 > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist >_______________________________________________ >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 shm37 at cam.ac.uk Mon Sep 28 01:20:28 2009 From: shm37 at cam.ac.uk (Stephen Montgomery) Date: Mon, 28 Sep 2009 11:20:28 +0300 Subject: [Mesquitelist] Ancestral state reconstructions Message-ID: <00a901ca4014$89d8a280$bb6f6f83@nimzoo04> Dear All, I am using Mesquite to do some ancestral state reconstructions of continuous data and I was hoping someone would be able to help with this query. I was wondering if it is possible to exclude a species' value from a dataset and use Mesquite to estimate that missing tip value so that it could be compared to the real data? If anyone knows whether or not this is possible, and if so how to do it, that would be a great help. Many thanks, Stephen Stephen Montgomery Evolutionary Genetics Group Dept. Zoology University of Cambridge -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090928/ea0ae654/attachment.html