From dag23 at duke.edu Mon Aug 10 13:52:56 2009 From: dag23 at duke.edu (David Garfield) Date: Mon, 10 Aug 2009 16:52:56 -0400 Subject: [Mesquitelist] Creating character states/partitions Message-ID: <8FD06A62-CF06-4CFC-92E8-7CB65DAEB4D5@duke.edu> Hi list, I'm a new user to Mesquite and may be missing something obvious, but I am having a hard time figuring out how to create character partitions from the GUI. I have sequences from several individuals for a cis- regulatory region and I would like to annotate/denote/partition out the small regions of this regulatory region that contain known transcription factor binding sites. Is there a way to select a group of characters (over all taxa) in the Character Matrix and create a partition? Thanks, David dag23 at duke.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090810/c5c34a32/attachment.html From catfish at mail.utexas.edu Tue Aug 11 08:45:53 2009 From: catfish at mail.utexas.edu (David Cannatella) Date: Tue, 11 Aug 2009 10:45:53 -0500 Subject: [Mesquitelist] retention index in Mesquite? Message-ID: <4134E258-3037-459D-B7E1-4383D117A9A6@mail.utexas.edu> For some reason, I'm unable to find how to calculate the retention index and consistency index in Mesquite, after about 45 minutes of searching (including the manual and the web help section on "Studying the History of Character Evolution". I can't find a match in my search for "retention." It must be there, right? Any ideas? Dave 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 Thu Aug 13 17:26:44 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 13 Aug 2009 17:26:44 -0700 Subject: [Mesquitelist] Assigning Group IDs In-Reply-To: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> References: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> Message-ID: First let me apologize for the late reply; I was in the field all of July and have taken a while to catch up. There is no direct way to paste in the group names in Mesquite. But there is a way to do it if you are willing to edit some text files, as per Kip's suggestion. Here is the step by step procedure. First, in Mesquite, define the group names in the List of Taxa window, Groups column. Best to use names without spaces or punctuation. (You can edit the names after you're done.) Assign a few taxa to groups (this just sets up the nexus file for you). Next in Excel have your taxa in the same order as in Mesquite. Add a column for the group. It sounds like you already have this. Add another column for the taxon number: Cat Carnivora 1 Cow Ungulata 2 Goat Ungulata 3 Dog Carnivora 4 Now cut out all columns except the group and number column: Carnivora 1 Ungulata 2 Ungulata 3 Carnivora 4 Save the file as a tab delimited text file. Open in a text editor that permits you to search and replace tabs and end of line characters. Replace all tabs by ": ", and all end of line characters by ", ". You should end up with a single line like this: Carnivora : 1, Ungulata : 2, Ungulata : 3, Carnivora: 4 Now open up your data file, saved by Mesquite as a NEXUS file (the default), in your text editor. You should see a block like this: BEGIN SETS; TAXPARTITION * UNTITLED = Carnivora : 1; END;. where "Carnivora: 1" will be different, depending on what few taxa you had assigned to groups. Simply replace this by the line you created from Excel. Reread the file, and it should work. Sorry this is a bit complex, and probably too late to be useful for you.... Wayne At 3:44 PM -0500 6.7.2009, JARRIN VALLADARES PABLO SANTIAGO wrote: >Content-type: multipart/alternative; > boundary="Boundary_(ID_XskKjVpgDWlE4xvoCAqIMA)" >Content-class: urn:content-classes:message > >Dear Friends, > >Is there a way to assign group partitions by pasting from an >external list (e.g. Excel)? With hundreds of sequences and many >groups this task results impossible to do manually. I have tried to >paste such a list with group assignments to no avail. > >Any suggestions are appreciated, thank you. > >Pablo > >Pablo Jarrin >Ph. D. candidate >Dept. of Biology / Boston University >M. A. Ecology Behavior and Evolution >Boston Univ. >Director Cient?fico >Estaci?n Cient?fica Yasun? >Escuela de Ciencias Biol?gicas >Pont. Univ. Cat?lica del Ecuador. > > >_______________________________________________ >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 Aug 13 17:26:52 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 13 Aug 2009 17:26:52 -0700 Subject: [Mesquitelist] Generating all possible resolutions for a polytomy In-Reply-To: References: Message-ID: No, you can't generate all possible alternative resolutions. You can sample them randomly (show tree in tree window, then use Randomly Modify Current Tree>Randomly Resolve Polytomies as a tree source for a second tree window or for Make New Tree Block from... Wayne At 3:24 PM +0800 10.7.2009, Jonah Choiniere wrote: >Hello all, > >I have a consensus tree with polytomies that I imported into Mesquite >from another program. Does anyone know of a way to automatically >generate a set of trees with all possible alternative resolutions of >the polytomies? > >Thanks, >Jonah > >-- >Jonah Choiniere >Ph.D. Candidate >The George Washington University >Robert Weintraub Program in Systematics and Evolution >_______________________________________________ >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 Aug 13 17:27:18 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 13 Aug 2009 17:27:18 -0700 Subject: [Mesquitelist] Creating character states/partitions In-Reply-To: <8FD06A62-CF06-4CFC-92E8-7CB65DAEB4D5@duke.edu> References: <8FD06A62-CF06-4CFC-92E8-7CB65DAEB4D5@duke.edu> Message-ID: An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090813/3f743f07/attachment.html From wmaddisn at interchange.ubc.ca Thu Aug 13 17:27:18 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 13 Aug 2009 17:27:18 -0700 Subject: [Mesquitelist] retention index in Mesquite? In-Reply-To: <4134E258-3037-459D-B7E1-4383D117A9A6@mail.utexas.edu> References: <4134E258-3037-459D-B7E1-4383D117A9A6@mail.utexas.edu> Message-ID: At 10:45 AM -0500 11.8.2009, David Cannatella wrote: >For some reason, I'm unable to find how to calculate the retention >index and consistency index in Mesquite, after about 45 minutes of >searching (including the manual and the web help section on "Studying >the History of Character Evolution". > >I can't find a match in my search for "retention." > >It must be there, right? Nope. The problem is that these aren't easy to calculate properly, and we haven't yet done them in Mesquite. It is especially hard to calculate the "maximum possible number of steps" for characters that are governed by a stepmatrix and which have polymorphic terminal taxa. If there's an outcry we could put them on our list... Wayne >Any ideas? > >Dave > >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 hulcr at wisc.edu Thu Aug 13 18:24:50 2009 From: hulcr at wisc.edu (Jiri Hulcr) Date: Thu, 13 Aug 2009 20:24:50 -0500 Subject: [Mesquitelist] FW: retention index in Mesquite? Message-ID: <25F3A39FE21F487CAECB4FF7B96717F4@Jiri> Hi, It seems that implementation of CI and RI into Mesquite are one of the most common requests on this listserv. I myself belong among the many people who would appreciate having these basic indices available in Mesquite, even if only for certain simpler kinds of phylogenies. Is it possible, eventually? Cheers, Jiri > -----Original Message----- > From: mesquitelist-bounces at mesquiteproject.org > [mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of Wayne > Maddison > Sent: Thursday, August 13, 2009 7:27 PM > To: David Cannatella > Cc: mesquitelist at mesquiteproject.org > Subject: Re: [Mesquitelist] retention index in Mesquite? > > At 10:45 AM -0500 11.8.2009, David Cannatella wrote: > >For some reason, I'm unable to find how to calculate the retention > >index and consistency index in Mesquite, after about 45 minutes of > >searching (including the manual and the web help section on > "Studying > >the History of Character Evolution". > > > >I can't find a match in my search for "retention." > > > >It must be there, right? > > Nope. The problem is that these aren't easy to calculate properly, > and we haven't yet done them in Mesquite. It is especially hard to > calculate the "maximum possible number of steps" for characters that > are governed by a stepmatrix and which have polymorphic terminal taxa. > > If there's an outcry we could put them on our list... > > Wayne > > >Any ideas? > > > >Dave > > > >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 > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From wmaddisn at interchange.ubc.ca Fri Aug 14 10:37:39 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri, 14 Aug 2009 10:37:39 -0700 Subject: [Mesquitelist] FW: retention index in Mesquite? In-Reply-To: <25F3A39FE21F487CAECB4FF7B96717F4@Jiri> References: <25F3A39FE21F487CAECB4FF7B96717F4@Jiri> Message-ID: The outcry (and a bit of groveling) have provoked me to think about this more carefully, and I realized it wasn't hard to add these to Mesquite by combining several calculations we already had. So, I've just built the modules for RI/CI for individual characters & a whole matrix. They will be in the next release. You might imagine that with something the size of Mesquite a difficult decision is what new features to even think about carefully. Once you spend the effort to think about them carefully, sometimes it turns out that they are easier than you had feared. When is the next release? Not sure. Sometime within the next few months, but we need to think about it carefully... Wayne At 8:24 PM -0500 13.8.2009, Jiri Hulcr wrote: >Hi, >It seems that implementation of CI and RI into Mesquite are one of the most >common requests on this listserv. I myself belong among the many people who >would appreciate having these basic indices available in Mesquite, even if >only for certain simpler kinds of phylogenies. Is it possible, eventually? >Cheers, >Jiri > > >> -----Original Message----- >> From: mesquitelist-bounces at mesquiteproject.org >> [mailto:mesquitelist-bounces at mesquiteproject.org] On Behalf Of Wayne >> Maddison >> Sent: Thursday, August 13, 2009 7:27 PM >> To: David Cannatella >> Cc: mesquitelist at mesquiteproject.org >> Subject: Re: [Mesquitelist] retention index in Mesquite? >> >> At 10:45 AM -0500 11.8.2009, David Cannatella wrote: >> >For some reason, I'm unable to find how to calculate the retention >> >index and consistency index in Mesquite, after about 45 minutes of >> >searching (including the manual and the web help section on >> "Studying >> >the History of Character Evolution". >> > >> >I can't find a match in my search for "retention." >> > >> >It must be there, right? >> >> Nope. The problem is that these aren't easy to calculate properly, >> and we haven't yet done them in Mesquite. It is especially hard to >> calculate the "maximum possible number of steps" for characters that >> are governed by a stepmatrix and which have polymorphic terminal taxa. >> >> If there's an outcry we could put them on our list... >> >> Wayne >> >> >Any ideas? >> > >> >Dave >> > >> >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 >> _______________________________________________ >> 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 KHayden at bennington.edu Mon Aug 17 10:05:08 2009 From: KHayden at bennington.edu (Hayden, Katherine M.) Date: Mon, 17 Aug 2009 13:05:08 -0400 Subject: [Mesquitelist] GSoC Project complete: Build a Mesquite Package to view Phenex-generated Nexml files Message-ID: <36DB60B1B53C764F9041382C4BCD67030162CB7D@ex01.bennington.edu> Hello list, My completed Google Summer of Code project, to build a Mesquite Package to view Phenex-generated Nexml files, can be found: Project page: https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Build_a_Mesquite_Package_to_view_Phenex-generated_Nexml_files Code: http://code.google.com/p/mesquitegsoc09/ The code includes an Installation folder containing setup instructions and necessary zipped files and jars. It was so great working with everyone during this GSoC and I'm incredibly thankful to everyone who made this experience what is was. Specifically, thanks to Peter, my mentor, Rutger, who answered a lot of nexml questions and, of course, Hilmar for being an excellent project leader. It probably goes without saying, but I'm definitely applying to GSoC next year as well. Thanks and best wishes, Kasia Katherine "Kasia" Hayden Bennington College, Class of 2011 312.576.8175 khayden at bennington.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090817/34934863/attachment.html From firestone2003 at yahoo.com Tue Aug 18 12:44:08 2009 From: firestone2003 at yahoo.com (Noah Firestone) Date: Tue, 18 Aug 2009 12:44:08 -0700 (PDT) Subject: [Mesquitelist] (no subject) Message-ID: <709837.85324.qm@web56105.mail.re3.yahoo.com> Hello, I have been having some trouble using Clustal on a mac OS 10.5.? I have the latest version of Java installed.? What happens, is I tell mesquite to clustal align, and a window comes up that says "command executing" and then the program stalls.? It doesn't matter if I do the alignment in the same thread or start a new thread.? I am using the latest version of mesquite as well; the program used to work just fine, and suddenly it stopped functioning properly.? I can run the alignment on clustal seperately, but the two programs don't seem to be running in conjunction. cheers, Noah -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090818/2567f441/attachment.html From catfish at mail.utexas.edu Sun Aug 23 10:05:54 2009 From: catfish at mail.utexas.edu (David Cannatella) Date: Sun, 23 Aug 2009 12:05:54 -0500 Subject: [Mesquitelist] Merge Taxa command Message-ID: <771AA30C-14DC-4742-9CF3-3EE9E1E27039@mail.utexas.edu> Another contrast between MacClade and Mesquite. For various reasons it is useful to merge taxa that have non- overlapping character vectors, as in the case where there are two fragments of the 12S-16S that have been sequenced for the same species. In MacClade, Merge Taxa would simply concatenate the entire taxon name of both. This was useful, because I could then edit down the name to keep the info I needed, such as the species name and the two different GenBank accession numbers. However, Mesquite truncates the taxon name of each to about the first 15 characters. This is much less useful, because I then have to go back and add in the information that was lost. Can I request that Mesquite be modified to simply concat the entirety of both names, and then allow the user to edit as needed? Thanks, Dave 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 beetle at ag.arizona.edu Mon Aug 24 10:02:03 2009 From: beetle at ag.arizona.edu (David Maddison) Date: Mon, 24 Aug 2009 10:02:03 -0700 Subject: [Mesquitelist] Merge Taxa command In-Reply-To: <771AA30C-14DC-4742-9CF3-3EE9E1E27039@mail.utexas.edu> References: <771AA30C-14DC-4742-9CF3-3EE9E1E27039@mail.utexas.edu> Message-ID: Dave, I've just changed Merge Taxa in Mesquite so that you now have the following options: (1) keep entire length of all taxon names, (2) only keep the first X characters and last Y characters of each taxon name. I could make it more flexible, such that it could keep the first A words and last B words of the name, but let's start with what I've done and see how it goes. This modified version is available right now for any of you who have checked out the latest source from the SVN repository; for everyone else, it will come out in Mesquite 2.7, RSN ("real soon now"). David -- =================================================================== David R. Maddison Professor and Curator PHONE: (520) 621 9781 Department of Entomology FAX: (520) 621 1150 University of Arizona email: beetle at ag.arizona.edu Tucson, AZ 85721 U.S.A. home page: http://david.bembidion.org Tree of Life: http://tolweb.org Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Address as of 16 September 2009: Department of Zoology 3029 Cordley Hall Oregon State University Corvallis, OR 97331 email: david.maddison at science.oregonstate.edu =================================================================== From wmaddisn at interchange.ubc.ca Tue Aug 25 11:36:09 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Tue, 25 Aug 2009 11:36:09 -0700 Subject: [Mesquitelist] Fixing states at nodes Message-ID: An off-list query about fixing ancestral states provokes me to give a hint to those of you on the list. For ancestral state reconstructions, you can't yet fix the state at a node directly. However you can "fake" it if you are using likelihood reconstructions, by adding a taxon that descends from the root and that has a very very very short branch, so that it effectively forces the root to match its state. In the attached, imagine that there are three real taxa. I've added a fourth, called "root", and made its branch length 0.000001, and made the length of the branch below the original root of the tree also 0.000001. This effectively places a state 0 at the original root of the tree. This trick does not work for parsimony, however, as parsimony does not pay attention to branch lengths. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: fixingRoot.jpg Type: application/octet-stream Size: 42483 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090825/06f48486/attachment-0001.obj From oakley at lifesci.ucsb.edu Tue Aug 25 11:51:25 2009 From: oakley at lifesci.ucsb.edu (Todd Oakley) Date: Tue, 25 Aug 2009 11:51:25 -0700 Subject: [Mesquitelist] Dollo-like ML/Fixing states at nodes In-Reply-To: References: Message-ID: <4A9432AD.5050000@lifesci.ucsb.edu> Thanks Wayne, Also as a similar tip, I've been creating Dollo-like ML models in the same way. Starting with an asymmetric model (binary/2-state), I create a new model, where the rate in 1 direction is estimated, and the rate in the other direction is set to ~0.0000001. It seems the calculations don't like to have a rate set all the way to zero (I'm not sure why though, the likelihood function should be fine with one rate set to zero). I've also checked this work-around, and the "dollo-like" model behaves as expected using stochastic character mapping and ancestral state estimations: character state transitions only go in one direction. Todd > An off-list query about fixing ancestral states provokes me to give a > hint to those of you on the list. For ancestral state > reconstructions, you can't yet fix the state at a node directly. > However you can "fake" it if you are using likelihood reconstructions, > by adding a taxon that descends from the root and that has a very very > very short branch, so that it effectively forces the root to match its > state. In the attached, imagine that there are three real taxa. I've > added a fourth, called "root", and made its branch length 0.000001, > and made the length of the branch below the original root of the tree > also 0.000001. This effectively places a state 0 at the original root > of the tree. This trick does not work for parsimony, however, as > parsimony does not pay attention to branch lengths. > > Wayne > > > ------------------------------------------------------------------------ > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist > -- ________________________________________ Todd H. Oakley Professor Ecology Evolution and Marine Biology University of California-Santa Barbara Santa Barbara, CA 93106 (805) 893-4715 http://www.lifesci.ucsb.edu/eemb/labs/oakley/ From beetle at ag.arizona.edu Tue Aug 25 17:12:31 2009 From: beetle at ag.arizona.edu (David Maddison) Date: Tue, 25 Aug 2009 17:12:31 -0700 Subject: [Mesquitelist] Clusal In-Reply-To: <709837.85324.qm@web56105.mail.re3.yahoo.com> References: <709837.85324.qm@web56105.mail.re3.yahoo.com> Message-ID: Noah, Are you using ClustalW, not ClustalX? This tool in Mesquite requires the command-line version of Clustal, and will show the behavior you describe if you are using ClustalX. If you *are* using ClustalW, then please send a note again. (I have no problems here using this with ClustalW and MacOS X 10.5.) David At 12:44 PM -0700 18/8/2009, Noah Firestone wrote: >Hello, >I have been having some trouble using Clustal on a mac OS 10.5. I >have the latest version of Java installed. What happens, is I tell >mesquite to clustal align, and a window comes up that says "command >executing" and then the program stalls. It doesn't matter if I do >the alignment in the same thread or start a new thread. I am using >the latest version of mesquite as well; the program used to work >just fine, and suddenly it stopped functioning properly. I can run >the alignment on clustal seperately, but the two programs don't seem >to be running in conjunction. >cheers, >Noah > > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- =================================================================== David R. Maddison Professor and Curator PHONE: (520) 621 9781 Department of Entomology FAX: (520) 621 1150 University of Arizona email: beetle at ag.arizona.edu Tucson, AZ 85721 U.S.A. home page: http://david.bembidion.org Tree of Life: http://tolweb.org Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Address as of 16 September 2009: Department of Zoology 3029 Cordley Hall Oregon State University Corvallis, OR 97331 email: david.maddison at science.oregonstate.edu =================================================================== From beetle at ag.arizona.edu Tue Aug 25 17:49:57 2009 From: beetle at ag.arizona.edu (David Maddison) Date: Tue, 25 Aug 2009 17:49:57 -0700 Subject: [Mesquitelist] Summarise State Changes Over Trees In-Reply-To: <1DAD2FCA-6E2C-473E-9395-C333DA7FD0F5@systbot.uzh.ch> References: <1DAD2FCA-6E2C-473E-9395-C333DA7FD0F5@systbot.uzh.ch> Message-ID: Aelys, At long last I have adjusted this. In the next version of Mesquite (2.7) you will be able to control what the maximum number of recorded changes is, so that you can increase it from 9 to, say, 20. Best wishes, David At 7:05 PM +0100 3/2/2009, Aelys Humphreys wrote: >Hello, > > Summarise State Changes Over Trees gives an >output of frequency of change between all states >and summarises it in terms of min, max and >average. It also displays the frequency of >number of changes (ie. in how many trees does a >certain transition change 0, 1, 2, 3, etc. >times). This is useful as you can then express >frequencies as percentiles rather than mean >values. Unfortunately, all frequencies above 9 >transitions are lumped, so that information is >lost if a character changes, say, 10-15 times >across the trees. Can this output can be >manipulated? > >many thanks, > >Aelys > >Aelys M. Humphreys, PhD Student >Institut f?r Systematische Botanik >Universit?t Z?rich >Zollikerstrasse 107 >CH-8008 Z?rich > >Email: aelys.humphreys at systbot.uzh.ch >Phone: +41 (0)44 634 8416 / 8411 / 8403 (fax) >Web: http://www.systbot.uzh.ch/ >/ http://www.systbot.uzh.ch/institut/personen/person.php?l=d&id=54 > > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist at mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- =================================================================== David R. Maddison Professor and Curator PHONE: (520) 621 9781 Department of Entomology FAX: (520) 621 1150 University of Arizona email: beetle at ag.arizona.edu Tucson, AZ 85721 U.S.A. home page: http://david.bembidion.org Tree of Life: http://tolweb.org Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Address as of 16 September 2009: Department of Zoology 3029 Cordley Hall Oregon State University Corvallis, OR 97331 email: david.maddison at science.oregonstate.edu =================================================================== From catfish at mail.utexas.edu Tue Aug 25 19:02:53 2009 From: catfish at mail.utexas.edu (David Cannatella) Date: Tue, 25 Aug 2009 21:02:53 -0500 Subject: [Mesquitelist] Clusal In-Reply-To: References: <709837.85324.qm@web56105.mail.re3.yahoo.com> Message-ID: <5F113CBD-5AB5-4203-8563-922F28C7E8F3@mail.utexas.edu> David, I've had a problem with using ClustalW, which is probably not related to Noah's problem. My path to ClustalW is: /Applications/Phylogeny Apps/Clustal2.0/clustalw2 I get the error message(s) below. In the Mesquite control window, there is a warning about a double //, but I can't figure out how to fix this: ======================================== (Separate Thread?) # (Mesquite) # (Clustal Locations & Options) # (Mesquite) # Exporting file to /Users/davidcannatella/ Mesquite_Support_Files/Mesquite_Prefs/temp/temp012354638739/ ClustalAlign/tempAlign01235464ce291516963933.nbrf Export complete. double // in path /Users/davidcannatella/Desktop/Ranines/ WiensRanidaeTree/Alignments/12S16S//Users/davidcannatella/ Mesquite_Support_Files/Mesquite_Prefs/temp/temp012354638739/ ClustalAlign/alignedFile01235464ce291516963933.nbrf ALERT: (Basic File Coordinator): A script refers to a linked file "/ Users/davidcannatella/Mesquite_Support_Files/Mesquite_Prefs/temp/ temp012354638739/ClustalAlign/alignedFile01235464ce291516963933.nbrf" that cannot be found. Because this linked file cannot be found, the remainder of the script might not execute properly, and various warning messages might be given. The probably cause of this is that someone saved a file with a second file linked, and then separated the two files. To avoid this problem in the future, either unlink files before saving, or maintain the linked file in the same relative position (e.g., in the same directory). (Alert) # (Mesquite) # double // in path /Users/davidcannatella/Desktop/Ranines/ WiensRanidaeTree/Alignments/12S16S//Users/davidcannatella/ Mesquite_Support_Files/Mesquite_Prefs/temp/temp012354638739/ ClustalAlign/alignedFile01235464ce291516963933.nbrf Note: File Busy or Not Found (0): directory file Align Sequences > doAlign "Clustal_Align" (Separate Thread?) # (Mesquite) # (Clustal Locations & Options) # (Mesquite) # ==================== And here are screen grabs of the other messages in the alert box and terminal window. Any thoughts? -------------- next part -------------- A non-text attachment was scrubbed... Name: pastedGraphic.jpg Type: image/jpeg Size: 153689 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090825/b8e6f78f/attachment-0001.jpg -------------- 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 On Aug 25, 2009, at 7:12 PM, David Maddison wrote: > Noah, > Are you using ClustalW, not ClustalX? This tool in Mesquite requires > the command-line version of Clustal, and will show the behavior you > describe if you are using ClustalX. If you *are* using ClustalW, > then please send a note again. > > (I have no problems here using this with ClustalW and MacOS X 10.5.) > > David > > At 12:44 PM -0700 18/8/2009, Noah Firestone wrote: >> Hello, >> I have been having some trouble using Clustal on a mac OS 10.5. I >> have the latest version of Java installed. What happens, is I tell >> mesquite to clustal align, and a window comes up that says "command >> executing" and then the program stalls. It doesn't matter if I do >> the alignment in the same thread or start a new thread. I am using >> the latest version of mesquite as well; the program used to work >> just fine, and suddenly it stopped functioning properly. I can run >> the alignment on clustal seperately, but the two programs don't seem >> to be running in conjunction. >> cheers, >> Noah >> >> >> _______________________________________________ >> Mesquitelist mailing list >> Mesquitelist at mesquiteproject.org >> http://mesquiteproject.org/mailman/listinfo/mesquitelist > > > -- > > =================================================================== > David R. Maddison > Professor and Curator PHONE: (520) 621 9781 > Department of Entomology FAX: (520) 621 1150 > University of Arizona email: beetle at ag.arizona.edu > Tucson, AZ 85721 U.S.A. > > home page: http://david.bembidion.org > Tree of Life: http://tolweb.org > Mesquite: http://mesquiteproject.org > MacClade: http://macclade.org > > Address as of 16 September 2009: > > Department of Zoology > 3029 Cordley Hall > Oregon State University > Corvallis, OR 97331 > > email: david.maddison at science.oregonstate.edu > > =================================================================== > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist From wmaddisn at interchange.ubc.ca Thu Aug 27 16:29:22 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Thu, 27 Aug 2009 16:29:22 -0700 Subject: [Mesquitelist] Mesquite 2.7 released Message-ID: Mesquite 2.7 has been released. A list of new features and important bug fixes is given at http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/changes.html. All users are urged to upgrade. Thanks for all of your bug reports and suggestions! -- ------------------------------------------------------------------- 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 wmaddisn at interchange.ubc.ca Sun Aug 30 22:41:41 2009 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Sun, 30 Aug 2009 22:41:41 -0700 Subject: [Mesquitelist] feedback on Mesquite 2.7 Message-ID: The "phone home" system Mesquite 2.7 has for reporting crashes is proving useful -- some crashes have already been logged on our server, and this will help us find and fix bugs. However, we have realized that we have no way currently of contacting you if Mesquite has submitted such a crash report. We will therefore add the option of your including your email address in the report, so that we can contact you with follow up questions to help us diagnose the issues. If you did have a crash, we would welcome an email from you to ensure we fix the problem. We anticipate that we will release a minor update over the next two weeks to fix the small bugs that have appeared. Please give us feedback soon as to how Mesquite 2.7 is behaving. Thanks! -- ------------------------------------------------------------------- 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