From rubentorices at gmail.com Mon Sep 8 02:13:05 2008 From: rubentorices at gmail.com (=?ISO-8859-1?Q?Rub=E9n_Torices_Blanco?=) Date: Mon, 8 Sep 2008 11:13:05 +0200 Subject: [Mesquitelist] Output all number of changes per mapping Message-ID: Dear Mesquite Users/Designers, I am studying the evolution of sexual systems in plants by reconstructing ancestral states. I am interested in what specific changes are inferred between all states and what are the quantitative importance of each change. For a matrix of categorical characters, how does one output a table that details the number of changes between states reconstructed? I see that Mesquite can output a table with minimum, maximum, and the average number of each change of states reconstructed over a set of trees (Taxa&Trees > Summarize States Changes Over Tree). However, I would like to output a table with all reconstructions instead of the average number. Each row will be one mapping per tree, and the columns will be the number of changes from one state to another state in that mapping. Then, I would like to study if the 95% of all mappings include zero changes between two states. Any ideas would be very welcome! I would appreciate any help with this, and thank you in advance. Rub?n Torices Blanco, Ph.D. Student ?rea de Biodiversidad y Conservaci?n Universidad Rey Juan Carlos c/ Tulip?n s/n., E-28933 M?stoles (Madrid) Spain-Espa?a Phone: +34 91 4888150 E-mail: ruben.torices at urjc.es -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080908/e22e0189/attachment.html From wmaddisn at interchange.ubc.ca Thu Sep 11 20:50:55 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:50:55 -0700 Subject: [Mesquitelist] ver 2.5: changing colors for character states? In-Reply-To: References: Message-ID: First, my apologies for being offline for so long. Field work, far away, followed by many trips. (This same apology is implicitly prepended to the other emails to follow soon.) If it's not too late to answer this: The instructions apply to Trace Character History. We have not yet extended this feature to Trace Character Over Trees. We'll put it on the To-do list. Wayne At 4:39 PM -0400 31.7.2008, Andrea Weeks wrote: >Hi there, > >I am having difficulty adjusting the colors that are assigned to >traced character states and wondered if there is a bug that is >preventing me from doing so. I am using the newest Mac OSX version. > >1) The directions "For categorical and molecular data, you can >change the colors used in Trace Character by double clicking on the >color rectangle in the Trace Legend. Revert to Default Colors is >available in the Trace menu." > >This doesn't work. Double clicking on the legend does nothing. >Control-clicking opens only Font/Size options. The "revert to >default colors" isn't listed in the Trace-over-Trees drop down menu. > >2) There are no apparent options in the Character Matrix Editor or >State Names Editor to adjust color of the states as they are traced >on a tree. > >Any insight on this would be greatly appreciated. > > >Andrea > >***************************************** >Assistant Professor, Plant Systematics >Director, Ted R. Bradley Herbarium >George Mason University >Department of Environmental Science and Policy, MSN 5F2 >4400 University Drive >Fairfax, Virginia 22030 USA >phone: (703) 993-3488 fax: (703) 993-1066 >lab web: http://mason.gmu.edu/~aweeks3/ >herbarium: http://www.gmu.edu/departments/espp/research/facilities/herbarium.html > > > > > > >_______________________________________________ >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 Sep 11 20:51:08 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:51:08 -0700 Subject: [Mesquitelist] triangle inequality In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080911/cb51a781/attachment.html From wmaddisn at interchange.ubc.ca Thu Sep 11 20:51:08 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:51:08 -0700 Subject: [Mesquitelist] script with mesquites In-Reply-To: <48A405F6.3040703@cs.rice.edu> References: <48A405F6.3040703@cs.rice.edu> Message-ID: I believe Cuong has figured this out (based on off-list emails), but I'll answer this for the sake of everyone else on the list. First, I'll explain why this doesn't work: tell mesquite.trees.SimulatedTreeBlocks.SimulatedTreeBlocks; setNumberTrees 10; endTell; "mesquite.trees.SimulatedTreeBlocks.SimulatedTreeBlocks" is the name of a kind (or class) of modules. It is not referring to a specific instance of this kind. In any run of Mesquite there could be several instances of this kind of module: one could be operating within one tree window, another could be operating within another tree window. You need to specify which instance of this kind of module you want. Why did your second snippet of script work? Here it is: getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; newTaxa 10 Species; endTell; All commands in the script are being sent to whichever object you are currently "telling". This is usually some module or another. Presumably in the context of this second snippet, you are speaking to the file coordinator module. The getEmployee command takes as its argument a kind of module. It says "return to me the instance of this kind of module that is your employee". Thus this command does return a particular instance, which can temporarily be referred to by "It". Thus, you really are commanding an instance in the second "tell". By the way, you can store "it" for later use as follows: getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; Object.taxonManager *it; . . . tell *Object.taxonManager; newTaxa 10 Species; endTell; Wayne At 5:16 AM -0500 14.8.2008, Cuong Than wrote: >Hello all, > >I have a very hard time using the scripting language of Mesquite. I >don't think the documentation on it is good and detailed. Here are some >problems I don't know to deal with, and I hope some of you can help me. > >- How can change the object to which I will send command to? As I know >from the documentation, it can be done with a 'tell' command. However, >this simply doesn't work in many cases. For example, I want to create a >block of trees, and I send the following script to Mesquite: > > tell mesquite.trees.SimulatedTreeBlocks.SimulatedTreeBlocks; > setNumberTrees 10; > endTell; > >Mesquite says it cannot execute the script returns a null object. > >- In another script, I want to create a group of 10 taxa: > > getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; > tell It; > newTaxa 10 Species; > endTell; > > >It worked, but I don't know why. > >I would like to thank you in advance for your help. >_______________________________________________ >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 Sep 11 20:51:08 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:51:08 -0700 Subject: [Mesquitelist] Java Heap Space out of memory In-Reply-To: References: <48A9152E.5000309@kimvdlinde.com> Message-ID: Thanks; we now have two reports of memory problems with the bucket. We suspect the bucket leaks. On the list to fix. Wayne At 8:46 AM +1000 19.8.2008, Buz Wilson wrote: >I had thought about increasing the heap size as a work-around - thanks >for the suggestion. My point, which I didn't describe clearly >(sorry...), was that I had been doing the same thing (filling cells with >a particular character state using the bucket tool) in the previous >version (2.0), and did not have this heap memory error & crash, using >the same data and the same startup defaults. I am also using the same >JRE installation. I'm building a large matrix, so not being able to use >the bucket tool seems somewhat retrogressive. So something seems to >have changed in the current Mesquite version that causes the problem -- >or maybe it was just because I was doing this on Monday... > >best wishes > >Buz > > >George D.F. (Buz) Wilson >Australian Museum (Marine Invertebrates) >6 College Street, Sydney 2010 Australia >tel: +612 9320 6287 >fax: +612 9320 6042 >email: buz.wilson at austmus.gov.au (Museum) >email2: buz at optusnet.com.au (home) > > > > >-----Original Message----- >From: Kim van der Linde [mailto:kim at kimvdlinde.com] >Sent: Monday, 18 August 2008 4:23 PM >To: Buz Wilson; mesquitelist at mesquiteproject.org >Subject: Re: [Mesquitelist] Java Heap Space out of memory > >java is reserving relative small amount of memory (heap size), but you >can increase it by using the following line: > >"C:\Program Files\Java\jdk1.4.2_17\bin\java.exe" -Xms1024m -Xmx1024m >mesquite.Mesquite > >Depending on the version of java you are using, you can go up a bit >more. If you have a 64-bit machine, you can go up substantially more. > >I use the above line in my shortcut, with "Start in" line: "C:\Program >Files\Mesquite" >##################################################################################### >This e-mail message has been scanned for Viruses and Content and cleared >by MailMarshal >##################################################################################### > >The Australian Museum. > >The views in this email are those of the user and do not necessarily >reflect the views of the Australian Museum. The information >contained in this email message and any accompanying files is or may >be confidential and is for the intended recipient only. If you are >not the intended recipient, any use, dissemination, reliance, >forwarding, printing or copying of this email or any attached files >is unauthorised. If you are not the intended recipient, please >delete it and notify the sender. The Australian Museum does not >guarantee the accuracy of any information contained in this e-mail >or attached files. As Internet communications are not secure, the >Australian Museum does not accept legal responsibility for the >contents of this message or attached files. >_______________________________________________ >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 Sep 11 20:51:08 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:51:08 -0700 Subject: [Mesquitelist] maximum likelihood values in ancestral reconstructions? In-Reply-To: References: Message-ID: From the manual (see http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/CharacterEvolution/AncestralStates.html), these paragraphs I believe answer your question: "Reporting of results: Likelihood ancestral state reconstructions can be reported in various ways. A first issue is whether only the best estimates are shown at a node or instead the support for each state is shown at a node, regardless of how strong or weak. This is controlled in Trace Character History by the Display Proportional to Weights menu item. If it is selected, then support for each state is shown; otherwise, only the states judged best are shown. The judgment of what are the best states is made according to a decision threshold T, such that if the log likelihoods of two states differ by T or more, the one with lower likelihood (higher negative log likelihood) is rejected. This is set using the Likelihood Decision Threshold menu item. What states are judged best can be viewed using Trace Character History in several ways: (1) When the cursor is held over a branch and the list of states appears at the bottom of the Trace Legend, the states judged best according to the threshold are marked with an asterisk; (2) In the Text view of the window, the list of reconstructions shows an asterisk by each state judged best at the mode; and (3) When Display Proportional to Weights is turned off, only the best states are shaded on the branches. The threshold and best states are also used in Trace Character Over Trees. Another issue is whether the likelihoods of alternative states are reported as is (Raw Likelihoods) or not. The other two options are to report proportional likelihoods (likelihoods of states are scaled so that they add up to 1, and thus for each state is shown its proportion of total likelihood) or negative log likelihoods. The former are convenient for interpretation and visualization; the latter may be more easily used in statistical tests. " The Report Likelihoods As menu item permits you to select raw/proportional/ -lnL. Thus, the asterisks do not quite indicate significance values, because there is not a formal statistical test here. Choosing between alternative states is not a situation of nested hypotheses where likelihood ratio tests (ln likelihood difference tests) can easily be done. Pagel has suggested a "rule of thumb" of a log likelihood difference of 2 indicating reasonable confidence. With scored character states in terminal taxa it is presumed your observation is accurate, so the likelihood is 1. We didn't want to put an asterisk there, because we didn't want to give the impression that Mesquite is reporting the results of a calculation; rather, confidence in this state is the responsibility of the user and his/her observations. Wayne At 6:19 AM -0400 19.8.2008, krushnamegh at mail.utexas.edu wrote: >i am studying the evolution of mimicry by reconstructing ancestral >states using the maximum likelihood criterion with one-parameter >Markov k-state model, implemented in Mesquite. on the phylogeny with >ancestral reconstructions, when i place the cursor over any of the >internal nodes, the "trace character" window lists all the character >states and gives values for each of those. for example, i have six >character states for a particular character, and a specific internal >node shows the following in the "trace character" window: > >0:0.0002364 >1:4.3728954467E-5 >2:4.7586737726E-5 >3:0.99771091* >4:0.00045689 >5:4.7679802321E-5 > >are these numbers maximum likelihood scores? what do the '*' mean in >this case? i presume that the '*' denotes some kind of statistical >significance but i am not very sure. is it a significant value (at p >< 0.05 or so) from a maximum likelihood model for a particular >character state (state 3 in the above case) not being the ancestral >state at that node? i am particularly confused because if any single >value in a given set of values is below ~0.85 or so, the highest >values that together make up >0.85 or so all get the *. for example: > >0:0.005565657 >1:0.71353937* >2:0.00670567 >3:0.26246278* >4:0.00614855 >5:0.00056387 > >further, the highest (and single) value i get when i place the >cursor over any of the extant species is 1, without an asterisk. for >example, for a particular species: > >5:1.0 > >if these are significant values of some sort, shouldn't the 1's also >have an asterisk in front of them? > >i would appreciate any help with this, and thank you in advance. >-- >Krushnamegh Kunte > >FAS Center for Systems Biology >Harvard University >Cambridge, MA 02138, USA > >Office: (617) 384-9920 >Cell: (512) 577-1370 >Fax: (617) 495-2196 >Email: KKunte at cgr.harvard.edu or krushnamegh at gmail.com > >Academic Website: >http://www.bio.utexas.edu/grad/krushnamegh/Moorings/AcademicsHome.htm >General Website: http://www.bio.utexas.edu/grad/krushnamegh/Moorings/index.htm > >_______________________________________________ >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 Sep 11 20:51:08 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 20:51:08 -0700 Subject: [Mesquitelist] Question about using Mesquite in an Introductory Biology Laboratory In-Reply-To: <003601c902f2$bad78f00$3086ad00$@edu> References: <003601c902f2$bad78f00$3086ad00$@edu> Message-ID: An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080911/1966ef07/attachment.html From wmaddisn at interchange.ubc.ca Thu Sep 11 22:38:10 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 11 Sep 2008 22:38:10 -0700 Subject: [Mesquitelist] Likelihood reconstruction of changes: how to generate a table? In-Reply-To: <2EB5DF1C-0449-4AE6-B6CB-6E0EE70729FE@nyu.edu> References: <2EB5DF1C-0449-4AE6-B6CB-6E0EE70729FE@nyu.edu> Message-ID: With likelihood it's not clear to me exactly how you'd do this. Likelihood doesn't measure the probability of a state's occurrence at a node, but rather the probability of observing the data given the state's occurrence at the node. We've never tried to calculate the likelihood of a change -- i.e. the probability of the data given a state change on a branch. An interesting idea, but I'm not aware that anyone has used the calculation. (It could be done relatively easily for categorical characters as a sum of node state likelihoods.) Would you be interested in the sum over all characters of the likelihoods of change on a branch? Another option would be to use stochastic character mapping to estimate distributions of total numbers of changes on a branch. This would involve a new module to sum over realizations. What exactly would you want? Wayne At 4:56 PM -0400 8.8.2008, David Fitch wrote: >Dear Mesquite Users/Designers, > >For a matrix of discrete binary characters, how does one output a >table that details the likelihood reconstruction of character-state >CHANGES ("losses" and "gains") in each character and each branch? > >I see that Mesquite can output a table of the probabilities of >HAVING a particular state at each branch for each character >(Analysis > TraceAllCharacters). And I see that Mesquite can output >a table of changes occurring across a (or many) tree(s) for ONE >particular character at a time (Taxa&Trees > >SummarizeStateChangesOverTrees). However, I cannot figure out how >to output a table of CHANGES for EACH branch for EACH character. > >For example, each character could be represented by a row in the table. >Each branch is represented by a pair of columns: > the 1st column with the number of gains, > the 2nd column with the number of losses. > >Presumably, the "number of gains" or "number of losses" would not >necessarily be integers, because the probability of a particular >change may not be 1.0 or 0.0 for a particular branch (unless the >decision threshold is applied; e.g. >50% probability for a gain >would be scored as a definite gain for that branch). > >Any ideas would be very welcome! >thanks, >David Fitch > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - - >~ David H. A. Fitch ~ \ / / / >~ Associate Professor ~ \/ / / >~ Department of Biology ~ \ / / >~ New York University ~ [] / / >~ Main Building, Room 1009 ~ \ / / >~ 100 Washington Square East ~ \/ / >~ New York, NY 10003 ~ \ / >~ U S A ~ \/ >~ Tel.: (212) 998-8254 ~ \ >~ Fax: (212) 995-4015 ~ \ >~ e-mail: david.fitch at nyu.edu ~ \ >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > http://www.nyu.edu/projects/fitch/ > > > > > >_______________________________________________ >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 rahmed01 at gmail.com Wed Sep 17 12:04:46 2008 From: rahmed01 at gmail.com (Rayhan Ahmed) Date: Wed, 17 Sep 2008 15:04:46 -0400 Subject: [Mesquitelist] triangle inequality In-Reply-To: References: Message-ID: i've gone ahead and purchased paup* to deal with this issue but for the future it would be nice for it to both check and the option for either user or program to fix. -ray On Thu, Sep 11, 2008 at 11:51 PM, Wayne Maddison < wmaddisn at interchange.ubc.ca> wrote: > No, Mesquite does not yet do checking of the triangle inequality. It's > good to know that there is interest in this. Would you want Mesquite to > check, or to check and fix? > > Wayne > > > At 5:58 PM -0500 11.8.2008, Rayhan Ahmed wrote: > > has the problem below been rectified - i'm looking to prepare a stepmatrix > from the Gonnet model of AA's but would like to correct for triangle > inequalities...w/o having to purchase paup4* > > any suggestions? > > -ray > > This stepmatrix editor does not do triangle inequality checking (see > discussion in manual of MacClade, which does check the triangle inequality). > > > _______________________________________________ > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080917/969e0047/attachment.html From ymwur1 at gmail.com Sat Sep 27 18:10:58 2008 From: ymwur1 at gmail.com (Hung Chih-Ming) Date: Sat, 27 Sep 2008 20:10:58 -0500 Subject: [Mesquitelist] bugs in Mesquite? Message-ID: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> Hi Mesquite users, I have a problem with using Mesquite in Window, and hope someone can give me some advise. I install Mesquite Version 2.5 in a computer with Window Vista Enterpirse. But I find all buttons, such as tree drawing fuctions, of several windows do not show the symbols on it. Although I may know the functions of buttons by the statement showing at the bottom of windows, it is very unconvient to use. Does nayone meet the same problem and know how to fix it? Thank you so much, Chih -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080927/1b274cc7/attachment.html From parsimony at earthlink.net Sat Sep 27 18:15:22 2008 From: parsimony at earthlink.net (greg) Date: Sat, 27 Sep 2008 18:15:22 -0700 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> References: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> Message-ID: <48DEDAAA.5040700@earthlink.net> get a mac Hung Chih-Ming wrote: > Hi Mesquite users, > > I have a problem with using Mesquite in Window, and hope someone can > give me some advise. I install Mesquite Version 2.5 in a computer with > Window Vista Enterpirse. But I find all buttons, such as tree drawing > fuctions, of several windows do not show the symbols on it. Although > I may know the functions of buttons by the statement showing at the > bottom of windows, it is very unconvient to use. Does nayone meet the > same problem and know how to fix it? > > Thank you so much, > > Chih > ------------------------------------------------------------------------ > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist > From ppdias at gmail.com Sat Sep 27 21:19:13 2008 From: ppdias at gmail.com (Pedro Dias) Date: Sun, 28 Sep 2008 01:19:13 -0300 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <48DEDAAA.5040700@earthlink.net> References: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> <48DEDAAA.5040700@earthlink.net> Message-ID: <94729ea80809272119h5ca5f2b9gf99e019ff5658391@mail.gmail.com> Dear Greg, I DO think this sort of response is neither constructive nor polite in any way. If you don't have anything to say that would help, please just don't do it. Chih: I hope some Windows users will be happy to help you (I'm a Linux user and have no Windows machine). Thanks, 2008/9/27 greg > get a mac > > Hung Chih-Ming wrote: > > Hi Mesquite users, > > > > I have a problem with using Mesquite in Window, and hope someone can > > give me some advise. I install Mesquite Version 2.5 in a computer with > > Window Vista Enterpirse. But I find all buttons, such as tree drawing > > fuctions, of several windows do not show the symbols on it. Although > > I may know the functions of buttons by the statement showing at the > > bottom of windows, it is very unconvient to use. Does nayone meet the > > same problem and know how to fix it? > > > > Thank you so much, > > > > Chih > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > -- ---------------------------------- Pedro Dias Laborat?rio de Sistem?tica Vegetal Departamento de Bot?nica Instituto de Bioci?ncias Universidade de S?o Paulo Rua do Mat?o, 277 05508-090 S?o Paulo-SP, Brazil Phone: +55 11 3091 7545 Fax: +55 11 3091 7547 Skype: ppdias http://web.ib.usp.br/~pdias Please avoid sending me Word, Excel or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080928/800ae6b4/attachment.html From tgarland at ucr.edu Sun Sep 28 05:30:32 2008 From: tgarland at ucr.edu (tgarland at ucr.edu) Date: Sun, 28 Sep 2008 05:30:32 -0700 (PDT) Subject: [Mesquitelist] bugs in Mesquite? Message-ID: <20080928053032.AIF66678@fmh.ucr.edu> Let's hope/presume that Greg had his tongue deeply in h= is cheek ... Cheers, Ted <= /DIV> 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 Associate Director Network for Experimental Research on Evolution http://nere.bio.uci.edu/ (A University of California Multicampus Research Project) ---- Original message ----
Date: Sun,= 28 Sep 2008 01:19:13 -0300 From: "Pedro Dias" Subject: Re: [Mesquitelist] bugs in Mesquite? = To: mesquitelist at mesquiteproject.org Dear Greg, I DO think this sort of response is nei= ther constructive nor polite in any way. If you don't have anything t= o say that would help, please just don't do it. Chih: I hope some= Windows users will be happy to help you (I'm a Linux user and have no W= indows machine). Thanks, 2008/9/27 greg <parsimony at earthl= ink.net> get a mac Hung Chih-Ming wrote: > Hi Mesquite users,> > I have a problem with using Mesquite in Window, and hope s= omeone can > give me some advise. I install Mesquite Version 2.5 i= n a computer with > Window Vista Enterpirse. But I find all = buttons, such as tree drawing > fuctions, of several windows do no= t show the symbols on it. Although > I may know the function= s of buttons by the statement showing at the > bottom of windows, = it is very unconvient to use. Does nayone meet the > same pr= oblem and know how to fix it? > > Thank you so much, > > Chih > -------------------------------------- ---------------------------------- > > _____________________= __________________________ > Mesquitelist mailing list > Mesquit= elist at mesquiteproject.org > http://mesquiteprojec t.org/mailman/listinfo/mesquitelist > _____________________= __________________________ Mesquitelist mailing list Mesquitelist at mesq= uiteproject.org http://mesquiteproject.org/mailman/l= istinfo/mesquitelist -= - ---------------------------------- Pedro Dias Laborat?rio = de Sistem?tica Vegetal Departamento de Bot?nica Instituto de B= ioci?ncias Universidade de S?o Paulo Rua do Mat?o, 277 05= 508-090 S?o Paulo-SP, Brazil Phone: +55 11 3091 7545 Fax: +55= 11 3091 7547 Skype: ppdias http://web.ib.usp.br/~pdias Please avoid se= nding me Word, Excel or PowerPoint attachments. See http:/= /www.gnu.org/philosophy/no-word-attachments.html >______= __________ >_______________________________________________ >Mesqu itelist mailing list >Mesquitelist at mesquiteproject.org >http://mes= quiteproject.org/mailman/listinfo/mesquitelist -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080928/49e24134/attachment.html From wmaddisn at interchange.ubc.ca Sun Sep 28 09:45:52 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 28 Sep 2008 09:45:52 -0700 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> References: <867157220809271810j2c93f397x494b95d29faf26e4@mail.gmail.com> Message-ID: Your problem is new to us. It sounds as if the installation did not proceed properly. First, could you send me a screenshot showing the problem? (Send it straight to me; no need to send it to the list.) Second, how many files are contained in the folder Mesquite_Folder/images? Is there a file Mesquite_Folder/images/arrow.gif, and can you open it in a graphics program? WAyne At 8:10 PM -0500 27.9.2008, Hung Chih-Ming wrote: >Hi Mesquite users, > >I have a problem with using Mesquite in Window, and hope someone can >give me some advise. I install Mesquite Version 2.5 in a computer >with Window Vista Enterpirse. But I find all buttons, such as tree >drawing fuctions, of several windows do not show the symbols on it. >Although I may know the functions of buttons by the statement >showing at the bottom of windows, it is very unconvient to use. >Does nayone meet the same problem and know how to fix it? > >Thank you so much, > >Chih > > >_______________________________________________ >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 kmagnacca at wesleyan.edu Sun Sep 28 10:03:32 2008 From: kmagnacca at wesleyan.edu (Karl Magnacca) Date: Sun, 28 Sep 2008 18:03:32 +0100 (IST) Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <20080928053032.AIF66678@fmh.ucr.edu> References: <20080928053032.AIF66678@fmh.ucr.edu> Message-ID: <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> On Sun, September 28, 2008 1:30 pm, tgarland at ucr.edu wrote: > Let's hope/presume that Greg had his tongue deeply in his > cheek ... Given the attitude one often gets from Mac users, I suspect not. Not that I'm defending how wonderful Windows is (especially not Vista), but it's funny how they always overlook the multitude of bugs that plague Macs as well. Karl ===================== Karl Magnacca Postdoctoral Researcher Department of Zoology Trinity College, Dublin 2 Ireland From wmaddisn at interchange.ubc.ca Sun Sep 28 10:44:50 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 28 Sep 2008 10:44:50 -0700 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> Message-ID: OK, no need to get into a Mac versus PC flame war. For what it's worth, Mesquite in the old days (ca. 1998-2003) behaved a bit better on Macs (there was one particularly nasty menu bug in Sun's Java on Windows). Then for several years (ca. 2003-2006) the speed was much better under Windows, and Mac Java had several glitches in graphics. For the last couple of years Mac OS X and Windows seem about equally good at running Mesquite. Does anyone have comments about installing or running Mesquite under Vista? Has it worked well for you, or are there "issues"? 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 sylvain at bergianska.se Sun Sep 28 23:33:01 2008 From: sylvain at bergianska.se (Sylvain Razafimandimbison) Date: Mon, 29 Sep 2008 08:33:01 +0200 Subject: [Mesquitelist] Bugs in Mesquite? In-Reply-To: References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> Message-ID: <114AF15A-5BF8-4C15-8B89-AAE10B8C84BF@bergianska.se> Dear Mesquite users, I am using Mesquite for the first time and find it very handy. What I really want to do is to run a correlation of analysis of the matrix attached to this email using Page94 model. Unfortunately, I keep getting the following alert message: "A command could not be completed because an exception occurred (i.e. a crash; class java.lang.ArrayindexOutOfBoundsException). If you save any filess, you might best use Save as.... in case file saving doesn't work properly". I am desperately need help because I have been stuck on this for a month. I wonder if my problem has to do with the number of taxa I have. Best regards, Sylvain -------------------------------------------------------------- Sylvain Razafimandimbison, Ph.D The Bergius Foundation, Royal Swedish Academy of Sciences, SE-10504, Stockholm, Sweden --------------------------------------------------------------- Mailing address: Department of Botany, Bergius Foundation, SE-10691, Stockholm University, Stockholm, Sweden On Sep 28, 2008, at 7:44 PM, Wayne Maddison wrote: > OK, no need to get into a Mac versus PC flame war. For what it's > worth, Mesquite in the old days (ca. 1998-2003) behaved a bit better > on Macs (there was one particularly nasty menu bug in Sun's Java on > Windows). Then for several years (ca. 2003-2006) the speed was much > better under Windows, and Mac Java had several glitches in graphics. > For the last couple of years Mac OS X and Windows seem about equally > good at running Mesquite. > > Does anyone have comments about installing or running Mesquite under > Vista? Has it worked well for you, or are there "issues"? > > 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 > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From wmaddisn at interchange.ubc.ca Mon Sep 29 07:28:39 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 29 Sep 2008 07:28:39 -0700 Subject: [Mesquitelist] Bugs in Mesquite? In-Reply-To: <114AF15A-5BF8-4C15-8B89-AAE10B8C84BF@bergianska.se> References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> <114AF15A-5BF8-4C15-8B89-AAE10B8C84BF@bergianska.se> Message-ID: Could you send the data file, as well as the contents of the log? (The message you quoted is just a portion of the error message; the rest of the message is in the log file.) thanks, Wayne At 8:33 AM +0200 29.9.2008, Sylvain Razafimandimbison wrote: >Dear Mesquite users, > >I am using Mesquite for the first time and find it very handy. What I >really want to do is to run a correlation of analysis of the matrix >attached to this email using Page94 model. Unfortunately, I keep >getting the following alert message: "A command could not be >completed because an exception occurred (i.e. a crash; class >java.lang.ArrayindexOutOfBoundsException). If you save any filess, >you might best use Save as.... in case file saving doesn't work >properly". I am desperately need help because I have been stuck on >this for a month. I wonder if my problem has to do with the number of >taxa I have. >Best regards, >Sylvain >-------------------------------------------------------------- >Sylvain Razafimandimbison, Ph.D >The Bergius Foundation, Royal Swedish Academy of Sciences, SE-10504, >Stockholm, >Sweden >--------------------------------------------------------------- >Mailing address: Department of Botany, Bergius Foundation, SE-10691, >Stockholm University, Stockholm, Sweden > > > > >On Sep 28, 2008, at 7:44 PM, Wayne Maddison wrote: > >> OK, no need to get into a Mac versus PC flame war. For what it's >> worth, Mesquite in the old days (ca. 1998-2003) behaved a bit better >> on Macs (there was one particularly nasty menu bug in Sun's Java on >> Windows). Then for several years (ca. 2003-2006) the speed was much >> better under Windows, and Mac Java had several glitches in graphics. >> For the last couple of years Mac OS X and Windows seem about equally >> good at running Mesquite. >> >> Does anyone have comments about installing or running Mesquite under >> Vista? Has it worked well for you, or are there "issues"? >> >> 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 >> _______________________________________________ >> 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 jd314704 at ohio.edu Mon Sep 29 11:48:19 2008 From: jd314704 at ohio.edu (jd314704 at ohio.edu) Date: Mon, 29 Sep 2008 14:48:19 -0400 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> <1222710235.48e113db661d2@webmail.ohio.edu> Message-ID: <1222714099.48e122f324318@webmail.ohio.edu> We've tried it in our lab on Vista machines and have noticed that happens sometimes when trying to open from the desktop icon. However, if you start it by opening the Run_mesquite_windows.bat file, the program opens correctly and there is no problem after that. Joe D. > > > > > >Quoting Wayne Maddison : > > > >> OK, no need to get into a Mac versus PC flame war. For what > it's > >> worth, Mesquite in the old days (ca. 1998-2003) behaved a bit > better > >> > >> on Macs (there was one particularly nasty menu bug in Sun's Java > on > >> Windows). Then for several years (ca. 2003-2006) the speed was > much > >> > >> better under Windows, and Mac Java had several glitches in > graphics. > >> > >> For the last couple of years Mac OS X and Windows seem about > equally > >> > >> good at running Mesquite. > >> > >> Does anyone have comments about installing or running Mesquite > under > >> > >> Vista? Has it worked well for you, or are there "issues"? > >> > >> 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 > >> _______________________________________________ > >> 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 jd314704 at ohio.edu Mon Sep 29 11:52:24 2008 From: jd314704 at ohio.edu (jd314704 at ohio.edu) Date: Mon, 29 Sep 2008 14:52:24 -0400 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> <1222710235.48e113db661d2@webmail.ohio.edu> Message-ID: <1222714344.48e123e80bc8a@webmail.ohio.edu> Ergh. Should know better than to try to email during an experiment. Apologies to those who get this twice. Anyway, below is how to deal with the Vista problem. Joe D. Quoting Wayne Maddison : > Thanks! There must be some issue with the installer. Could you send > > this response to the list? > Wayne > > >We've tried it in our lab on Vista machines and have noticed that > happens > >sometimes when trying to open from the desktop icon. However, if you > start it > >by opening the Run_mesquite_windows.bat file, the program opens > correctly and > >there is no problem after that. > > > >Joe D. > > > > > >Quoting Wayne Maddison : > > > >> OK, no need to get into a Mac versus PC flame war. For what > it's > >> worth, Mesquite in the old days (ca. 1998-2003) behaved a bit > better > >> > >> on Macs (there was one particularly nasty menu bug in Sun's Java > on > >> Windows). Then for several years (ca. 2003-2006) the speed was > much > >> > >> better under Windows, and Mac Java had several glitches in > graphics. > >> > >> For the last couple of years Mac OS X and Windows seem about > equally > >> > >> good at running Mesquite. > >> > >> Does anyone have comments about installing or running Mesquite > under > >> > >> Vista? Has it worked well for you, or are there "issues"? > >> > >> 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 > >> _______________________________________________ > >> 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 29 12:42:39 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Mon, 29 Sep 2008 12:42:39 -0700 Subject: [Mesquitelist] bugs in Mesquite? In-Reply-To: <1222714099.48e122f324318@webmail.ohio.edu> References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> <1222710235.48e113db661d2@webmail.ohio.edu> <1222714099.48e122f324318@webmail.ohio.edu> Message-ID: Thanks, Joe. It appears that the installer has problems under Vista. For our help in debugging this, has anyone ever had the installer work successfully under Vista, such that double clicking on the shortcut on the desktop does give a working version of Mesquite? Wayne At 2:48 PM -0400 29.9.2008, jd314704 at ohio.edu wrote: > >We've tried it in our lab on Vista machines and have noticed that > happens sometimes when trying to open from the desktop icon. However, if you > start it by opening the Run_mesquite_windows.bat file, the program opens > correctly and there is no problem after that. > >Joe D. -- -------------------------------------------------------- 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 Sep 30 07:52:18 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Tue, 30 Sep 2008 07:52:18 -0700 Subject: [Mesquitelist] Bugs in Mesquite? In-Reply-To: <114AF15A-5BF8-4C15-8B89-AAE10B8C84BF@bergianska.se> References: <20080928053032.AIF66678@fmh.ucr.edu> <36120.134.226.1.234.1222621412.squirrel@webmail.wesleyan.edu> <114AF15A-5BF8-4C15-8B89-AAE10B8C84BF@bergianska.se> Message-ID: Sylvan's problem arose because one of his characters had more than two states. The Pagel94 calculations require binary characters (states 0 and 1 only). Mesquite has a user interface bug, in that it should have gracefully warned the user that the character couldn't be used instead of the generating the exception. We'll fix that. Wayne At 8:33 AM +0200 29.9.2008, Sylvain Razafimandimbison wrote: >Dear Mesquite users, > >I am using Mesquite for the first time and find it very handy. What I >really want to do is to run a correlation of analysis of the matrix >attached to this email using Page94 model. Unfortunately, I keep >getting the following alert message: "A command could not be >completed because an exception occurred (i.e. a crash; class >java.lang.ArrayindexOutOfBoundsException). If you save any filess, >you might best use Save as.... in case file saving doesn't work >properly". I am desperately need help because I have been stuck on >this for a month. I wonder if my problem has to do with the number of >taxa I have. >Best regards, >Sylvain >-------------------------------------------------------------- >Sylvain Razafimandimbison, Ph.D >The Bergius Foundation, Royal Swedish Academy of Sciences, SE-10504, >Stockholm, >Sweden >--------------------------------------------------------------- >Mailing address: Department of Botany, Bergius Foundation, SE-10691, >Stockholm University, Stockholm, Sweden > > > > >On Sep 28, 2008, at 7:44 PM, Wayne Maddison wrote: > >> OK, no need to get into a Mac versus PC flame war. For what it's >> worth, Mesquite in the old days (ca. 1998-2003) behaved a bit better >> on Macs (there was one particularly nasty menu bug in Sun's Java on >> Windows). Then for several years (ca. 2003-2006) the speed was much >> better under Windows, and Mac Java had several glitches in graphics. >> For the last couple of years Mac OS X and Windows seem about equally >> good at running Mesquite. >> >> Does anyone have comments about installing or running Mesquite under >> Vista? Has it worked well for you, or are there "issues"? >> >> 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 >> _______________________________________________ >> 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 phylogeo at yahoo.com Tue Sep 30 12:41:43 2008 From: phylogeo at yahoo.com (Stewart Grant) Date: Tue, 30 Sep 2008 12:41:43 -0700 (PDT) Subject: [Mesquitelist] Mesquite on Vista Message-ID: <135946.18937.qm@web30002.mail.mud.yahoo.com> Hi Wayne, I've been working with Mesquite on a laptop run by Vista and haven't had any problems loading the program from a desktop shortcut. However, Mesquite will freeze up if I try to simulate too many sequence datasets, but thats another problem with memory unrelated to Vista. Cheers, Stew Grant University of Alaska Anchorage -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080930/ccdb1039/attachment.html From wmaddisn at interchange.ubc.ca Tue Sep 30 12:59:47 2008 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Tue, 30 Sep 2008 12:59:47 -0700 Subject: [Mesquitelist] Mesquite on Vista In-Reply-To: <135946.18937.qm@web30002.mail.mud.yahoo.com> References: <135946.18937.qm@web30002.mail.mud.yahoo.com> Message-ID: At 12:41 PM -0700 30.9.2008, Stewart Grant wrote: >Hi Wayne, > >I've been working with Mesquite on a laptop run by Vista and haven't >had any problems loading the program from a desktop shortcut. >However, Mesquite will freeze up if I try to simulate too many >sequence datasets, but thats another problem with memory unrelated >to Vista. Do you know how to increase memory? Open up Run_Mesquite_Windows.bat and change -Xmx400M to something bigger, say -Xmx800M and then double click Run_Mesquite_Windows.bat to start Mesquite. By the way, for Mac OS X 10.5 users, if you want to allocate more than 2GB of memory to Mesquite, you add -d64 to the command line startup. Wayne > >Cheers, >Stew Grant >University of Alaska Anchorage > >_______________________________________________ >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