From david.fitch at nyu.edu Fri Aug 8 13:56:45 2008 From: david.fitch at nyu.edu (David Fitch) Date: Fri, 8 Aug 2008 16:56:45 -0400 Subject: [Mesquitelist] Likelihood reconstruction of changes: how to generate a table? Message-ID: <2EB5DF1C-0449-4AE6-B6CB-6E0EE70729FE@nyu.edu> 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080808/566f4c29/attachment.html From rahmed01 at gmail.com Mon Aug 11 15:58:05 2008 From: rahmed01 at gmail.com (Rayhan Ahmed) Date: Mon, 11 Aug 2008 17:58:05 -0500 Subject: [Mesquitelist] triangle inequality Message-ID: 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). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080811/9dc185d2/attachment.html From cvthan at cs.rice.edu Thu Aug 14 03:16:22 2008 From: cvthan at cs.rice.edu (Cuong Than) Date: Thu, 14 Aug 2008 05:16:22 -0500 Subject: [Mesquitelist] script with mesquites Message-ID: <48A405F6.3040703@cs.rice.edu> 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. From david.fitch at nyu.edu Thu Aug 14 07:16:48 2008 From: david.fitch at nyu.edu (David Fitch) Date: Thu, 14 Aug 2008 10:16:48 -0400 Subject: [Mesquitelist] likelihood reconstruction of CHANGES as well as states In-Reply-To: References: <407A4B3A-863C-4129-B4C3-A5DFA7EA306F@nyu.edu> <832B942E-D35C-4FB1-9423-0848BE4EDFEE@nyu.edu> Message-ID: <83FC5A86-4C8E-4402-9B8C-45B2F81BFB3C@nyu.edu> Dear Mesquite Users/Designers, For a matrix of categorical (discrete) binary characters, how does one output a table that details the likelihood reconstruction of character-state CHANGE PROBABILITIES ("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), which apparently depends on the "Likelihood Decision Threshold". However, I cannot figure out how to output a table of CHANGE PROBABILITIES for EACH branch for EACH character. In the table I envision, for example, each character would be represented by a row. Each branch (node) would be represented by a pair of columns: the 1st column with the number of (or probability of) gains, the 2nd column with the number of (or probability of) losses. 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080814/078ab53c/attachment.html From michel.laurin at upmc.fr Thu Aug 14 06:41:16 2008 From: michel.laurin at upmc.fr (Michel Laurin) Date: Thu, 14 Aug 2008 15:41:16 +0200 Subject: [Mesquitelist] script with mesquites In-Reply-To: <48A405F6.3040703@cs.rice.edu> References: <48A405F6.3040703@cs.rice.edu> Message-ID: Hello Than, For this, you don't need to script at all. Just use the menus to ask Mesquite to create a new block of trees, or to create a group of 10 taxa. Why would you want to write a script if the command is available, already? Of course, that might occur as part of a larger script. Is this what you want to do? If you need more info on the menus, just write to me off-list. And if you do need to script, I will have to led others anwer because I haven't mastered that either. Best, Michel >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 -- Michel Laurin CNRS UMR 7179 Universit? Paris 6 - Pierre et Marie Curie 4, place Jussieu case 19 75005 Paris FRANCE tel./fax. (33 1) 44 27 36 92 http://tolweb.org/notes/?note_id=3669 From Buz.Wilson at austmus.gov.au Sun Aug 17 20:49:28 2008 From: Buz.Wilson at austmus.gov.au (Buz Wilson) Date: Mon, 18 Aug 2008 13:49:28 +1000 Subject: [Mesquitelist] Java Heap Space out of memory Message-ID: I just upgraded Mesquite to 2.5 from the website today, and I am getting a out of memory problem when using the character state bucket tool. The console displays java exeption notices relating to memory or heap memory, everything freezes, and eventually Java and Mesquite crashes. Everything not saved is gone... This is a fairly small matrix with only 75 taxa and around 300 characters, so I don't know why it would have a problem. I'm running it on Windows XP machine with 2GB memory. Haven't tried it on Linux yet. Anyone else having problems? 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) ##################################################################################### 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080818/99e63f14/attachment.html From kim at kimvdlinde.com Sun Aug 17 23:22:38 2008 From: kim at kimvdlinde.com (Kim van der Linde) Date: Mon, 18 Aug 2008 02:22:38 -0400 Subject: [Mesquitelist] Java Heap Space out of memory In-Reply-To: References: Message-ID: <48A9152E.5000309@kimvdlinde.com> 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" Hope this helps. Kim Buz Wilson wrote: > I just upgraded Mesquite to 2.5 from the website today, and I am getting > a out of memory problem when using the character state bucket tool. The > console displays java exeption notices relating to memory or heap > memory, everything freezes, and eventually Java and Mesquite crashes. > Everything not saved is gone... > > > > This is a fairly small matrix with only 75 taxa and around 300 > characters, so I don?t know why it would have a problem. I?m running it > on Windows XP machine with 2GB memory. Haven?t tried it on Linux yet. > > > > Anyone else having problems? > > > > 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) > > > > ------------------------------------------------------------------------ > 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 -- http://www.kimvdlinde.com From Buz.Wilson at austmus.gov.au Mon Aug 18 15:46:48 2008 From: Buz.Wilson at austmus.gov.au (Buz Wilson) Date: Tue, 19 Aug 2008 08:46:48 +1000 Subject: [Mesquitelist] Java Heap Space out of memory In-Reply-To: <48A9152E.5000309@kimvdlinde.com> References: <48A9152E.5000309@kimvdlinde.com> Message-ID: 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. From krushnamegh at mail.utexas.edu Tue Aug 19 03:19:16 2008 From: krushnamegh at mail.utexas.edu (krushnamegh at mail.utexas.edu) Date: Tue, 19 Aug 2008 06:19:16 -0400 Subject: [Mesquitelist] maximum likelihood values in ancestral reconstructions? In-Reply-To: References: Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080819/23b9a73f/attachment.html From rxl5 at psu.edu Wed Aug 20 11:29:49 2008 From: rxl5 at psu.edu (Robert E. Loeb) Date: Wed, 20 Aug 2008 14:29:49 -0400 Subject: [Mesquitelist] Question about using Mesquite in an Introductory Biology Laboratory Message-ID: <003601c902f2$bad78f00$3086ad00$@edu> Colleagues, I am new to the list, so please excuse my ignorance if the questions I ask have been answered before. The introductory Biology class (first semester course) I will teach for the first time this semester provides an overview of phylogeny for about a third of the course. I was introduced to Mesquite at a program on Cladistics offered by the American Museum of Natural History for High School Teachers and want to incorporate the use of Mesquite in the laboratory. Has anyone developed laboratory exercises for an Introductory Biology course using Mesquite that you (they) would be willing to share? Another related question, since my small campus has few specimens, I wanted to use Excel spreadsheets containing morphological (in the case microbes, cytological) characteristics for groups so that the students could use for analysis in Mesquite. In advance, thanks for your assistance. Best, Rob Robert Loeb, Ph.D. Kenan Fellow National Tropical Botanical Gardens Associate Professor of Biology and Forestry Penn State DuBois College Place DuBois, PA 15801 814-375-4707 814-375-4724 (FAX) Personal Web Site: http://www.personal.psu.edu/rxl5/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080820/02aae74d/attachment.html From david.fitch at nyu.edu Wed Aug 20 13:47:28 2008 From: david.fitch at nyu.edu (David Fitch) Date: Wed, 20 Aug 2008 16:47:28 -0400 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: Hi Rob, while Mesquite is a great program, it is not so user friendly for first-time users, and I would not recommend it for a high school (or even undergrad) intro bio class. MacClade is much more user friendly, and Sinauer (the publisher) is willing to offer a nice license package for classes. Actually, I use MacClade even in my graduate course (along with PAUP*). But before we do that, we test alternative phylogenetic hypotheses by HAND. The sample morphological matrix "Vertebrates" that comes with MacClade is excellent for this, but you can also use sample molecular sequences. I use a matrix with 5 taxa and 10 nucleotide positions for students to use with UPGMA and parsimony methods by hand (limiting the analysis to 5 taxa allows students to test all 15 possible unrooted hypotheses--a good exercise in applying scientific method as well!). An alternative to real organisms is to use cyber-organisms such as those generated by Richard Dawkins' Watchmaker program. These "creatures" have very simple "body plans" and students can easily parse them into characters with discrete states. In fact, this is a major skill that is important for students to develop--defining the characters and filling in the matrix with data. Each group of students can use the phylogeny function of Watchmaker to "evolve" a set of taxa. The pictures of these taxa can then be given to other groups of students to see if they can infer the correct phylogeny. Taking the students through all these steps of systematics analysis-- from organism to characters to phylogeny (and even using the phylogeny to infer the evolution of other characters)--provides the students with a deeper appreciation for the science than just having them infer phylogenies from data already given to them. good luck! David Fitch On Aug 20, 2008, at 2:29 PM, Robert E. Loeb wrote: > Colleagues, > > > > I am new to the list, so please excuse my ignorance if the > questions I ask have been answered before. > > > > The introductory Biology class (first semester course) I will teach > for the first time this semester provides an overview of phylogeny > for about a third of the course. I was introduced to Mesquite at a > program on Cladistics offered by the American Museum of Natural > History for High School Teachers and want to incorporate the use of > Mesquite in the laboratory. Has anyone developed laboratory > exercises for an Introductory Biology course using Mesquite that > you (they) would be willing to share? > > > > Another related question, since my small campus has few specimens, > I wanted to use Excel spreadsheets containing morphological (in the > case microbes, cytological) characteristics for groups so that the > students could use for analysis in Mesquite. > > > > In advance, thanks for your assistance. > > > > Best, > > Rob > > > > Robert Loeb, Ph.D. > > > > Kenan Fellow > > National Tropical Botanical Gardens > > > > Associate Professor of Biology and Forestry > > Penn State DuBois > > College Place > > DuBois, PA 15801 > > 814-375-4707 > > 814-375-4724 (FAX) > > Personal Web Site: http://www.personal.psu.edu/rxl5/ > > > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - - ~ 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/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080820/7b32141a/attachment.html From Buz.Wilson at austmus.gov.au Wed Aug 20 14:10:54 2008 From: Buz.Wilson at austmus.gov.au (Buz Wilson) Date: Thu, 21 Aug 2008 07:10:54 +1000 Subject: [Mesquitelist] Mesquite in a Biology Lab References: Message-ID: Peter Weston at Royal Botanic Gardens Sydney and I developed some simple sessions to teach phylogenetics using Mesquite and PAUP to relatively untrained students, some of whom were naive computer users. This was part of our ongoing collaboration with the University of New England in systematics theory training as part of a 3rd year course. This was an upgrade and shortening of a previous version that used DELTA and MacClade and PAUP. Overall it went reasonably well, although inexperience with biology and computers created some difficulties. If you have a more homogeneous group of students (we did not!) this should work reasonably well. Please contact me off list if you want more information. For the future, we will drop PAUP entirely and move to a more platform-independent system using (e.g.) TNT and POY with Mesquite so that the students can use either Linux*, PCs or Max. Incidently, I recommend you drop the spreadsheet entirely, as Mesquite will provide that facility, and you won't have to convert data from one format to another. Best wishes Buz *has anyone tried Mesquite on the EeePC? 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) ________________________________ From: mesquitelist-bounces at mesquiteproject.org on behalf of mesquitelist-request at mesquiteproject.org Sent: Thu 8/21/2008 5:00 AM To: mesquitelist at mesquiteproject.org Subject: Mesquitelist Digest, Vol 28, Issue 7 Send Mesquitelist mailing list submissions to mesquitelist at mesquiteproject.org To subscribe or unsubscribe via the World Wide Web, visit http://mesquiteproject.org/mailman/listinfo/mesquitelist or, via email, send a message with subject or body 'help' to mesquitelist-request at mesquiteproject.org You can reach the person managing the list at mesquitelist-owner at mesquiteproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Mesquitelist digest..." Today's Topics: 1. Question about using Mesquite in an Introductory Biology Laboratory (Robert E. Loeb) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Aug 2008 14:29:49 -0400 From: "Robert E. Loeb" Subject: [Mesquitelist] Question about using Mesquite in an Introductory Question about using Mesquite in an Introductory Biology Laboratory To: Message-ID: <003601c902f2$bad78f00$3086ad00$@edu> Content-Type: text/plain; charset="us-ascii" Colleagues, I am new to the list, so please excuse my ignorance if the questions I ask have been answered before. The introductory Biology class (first semester course) I will teach for the first time this semester provides an overview of phylogeny for about a third of the course. I was introduced to Mesquite at a program on Cladistics offered by the American Museum of Natural History for High School Teachers and want to incorporate the use of Mesquite in the laboratory. Has anyone developed laboratory exercises for an Introductory Biology course using Mesquite that you (they) would be willing to share? Another related question, since my small campus has few specimens, I wanted to use Excel spreadsheets containing morphological (in the case microbes, cytological) characteristics for groups so that the students could use for analysis in Mesquite. In advance, thanks for your assistance. Best, Rob Robert Loeb, Ph.D. Kenan Fellow National Tropical Botanical Gardens Associate Professor of Biology and Forestry Penn State DuBois College Place DuBois, PA 15801 814-375-4707 814-375-4724 (FAX) Personal Web Site: http://www.personal.psu.edu/rxl5/ -------------- next part -------------- An HTML attachment was scrubbed... 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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. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 9538 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080821/ac08212e/attachment-0001.bin