From marcin.czarnoleski at uj.edu.pl Mon Feb 8 03:43:46 2010 From: marcin.czarnoleski at uj.edu.pl (Marcin Czarnoleski) Date: Mon, 08 Feb 2010 12:43:46 +0100 Subject: [Mesquitelist] phylogenetically corrected PCA Message-ID: <4B6FF8F2.7080407@uj.edu.pl> Hi, I would be grateful for an advice how to solve my problem with phyllogenetic analysis pased on PCA (possibly with Mesquite). I use data on some traits of several species. I would like to use PCA to calculate PC scores from these traits, and use these scores to correlate with other characters of the species. But I would like to correct my analysis on a phylogentic signal. So basically, I should calculate phylogenetically corrected PC scores and then correlate them with contrasts of other species characters. But I have a question, should I first run PCA on raw data, and then calculate contrasts of the PC scores obtained from this PCA, and finally use these contrasts in correlattions with contrasts of other characters of species. Or alternativelly, I should run PCA on contrasts of species traits, and then use scores of these PCs to correlate them with contrasts of other charactes of species? If the second approach is recommended then I see two problems. First, to run PCA on contrasts it is adviced to use correlation matrix from contrasts (but correlations are forced through 0 and positivised). If I calculate such matrix and use it as an input file for PCA in an ordinary statistical software, I am unable to calculate PC scores because the information about species (cases) is missing (correlation matrix provides PCA only with correlation coefficients). So withought the scores I cannot proceed further and test correlations between phylogenetically corrected PC scores and contrasts of other traist. Second, even if I was able to obtain phylogenetically corrected PC scores, how should I analyse their correlation with contrasts of other traits. I understand that a normal correlation on contrasts requires prior positivisation and forcing through 0, but I am not sure what should be done in terms of this requirement in the case of scores vs contrasts correlation. I should be grateful for any opinion on my problem and I would be also grateful for the information whether Mesquite can help solve my problem. Marcin Czarnoleski From alejandro.gonzalez at ebd.csic.es Mon Feb 8 04:13:09 2010 From: alejandro.gonzalez at ebd.csic.es (Alejandro Gonzalez V) Date: Mon, 8 Feb 2010 13:13:09 +0100 Subject: [Mesquitelist] phylogenetically corrected PCA In-Reply-To: <4B6FF8F2.7080407@uj.edu.pl> References: <4B6FF8F2.7080407@uj.edu.pl> Message-ID: <479B269D-A0B2-4C81-9EF1-4A1F91117087@ebd.csic.es> Hi Marcin, You should have a look at the following paper: Revell L. J. 2009 Size-correction and principal components for interspecific comparative studies. Evolution 63:3258-3268 Liam provides code in the paper to run Phylogenetic PCA on species data (not contrasts) in R and Matlab. It works well, I've used it myself. Cheers, Alejandro __________________________________ Alejandro Gonzalez Voyer Post-doc NEW ADDRESS & NEW E-MAIL Estaci?n Biol?gica de Do?ana (CSIC) Avenida Am?rico Vespucio s/n 41092 Sevilla Spain E-mail: alejandro.gonzalez at ebd.csic.es Tel: +34- 954 466700, ext 1749 Website (From my previous position): http://www.iee.uu.se/zooekol/default.php?type=personalpage&lang=en&id=146 On Feb 8, 2010, at 12:43 PM, Marcin Czarnoleski wrote: > Hi, > I would be grateful for an advice how to solve my problem with > phyllogenetic analysis pased on PCA (possibly with Mesquite). I use data > on some traits of several species. I would like to use PCA to calculate > PC scores from these traits, and use these scores to correlate with > other characters of the species. But I would like to correct my analysis > on a phylogentic signal. So basically, I should calculate > phylogenetically corrected PC scores and then correlate them with > contrasts of other species characters. But I have a question, should I > first run PCA on raw data, and then calculate contrasts of the PC scores > obtained from this PCA, and finally use these contrasts in correlattions > with contrasts of other characters of species. Or alternativelly, I > should run PCA on contrasts of species traits, and then use scores of > these PCs to correlate them with contrasts of other charactes of > species? If the second approach is recommended then I see two problems. > First, to run PCA on contrasts it is adviced to use correlation matrix > from contrasts (but correlations are forced through 0 and positivised). > If I calculate such matrix and use it as an input file for PCA in an > ordinary statistical software, I am unable to calculate PC scores > because the information about species (cases) is missing (correlation > matrix provides PCA only with correlation coefficients). So withought > the scores I cannot proceed further and test correlations between > phylogenetically corrected PC scores and contrasts of other traist. > Second, even if I was able to obtain phylogenetically corrected PC > scores, how should I analyse their correlation with contrasts of other > traits. I understand that a normal correlation on contrasts requires > prior positivisation and forcing through 0, but I am not sure what > should be done in terms of this requirement in the case of scores vs > contrasts correlation. I should be grateful for any opinion on my > problem and I would be also grateful for the information whether > Mesquite can help solve my problem. > Marcin Czarnoleski > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100208/3fb63ba3/attachment.html From ana.millanes at urjc.es Mon Feb 8 06:41:12 2010 From: ana.millanes at urjc.es (ana.millanes at urjc.es) Date: Mon, 08 Feb 2010 15:41:12 +0100 Subject: [Mesquitelist] full distribution of number of changes In-Reply-To: <4B6FF8F2.7080407@uj.edu.pl> References: <4B6FF8F2.7080407@uj.edu.pl> Message-ID: <20100208154112.14457jwyfnz82mio@webmail.urjc.es> Hello, I'd be grateful for any advice: I'm counting the amount of change in a character over a tree sample with Mesquite (using "Analyze"-"Other Analyses with trees"-"Summarize change in selected clade" I would like to obtain the full distribution of the number of changes across the tree sample (i. e., X trees say there was 1 change, Y trees there were 2 changes, etc). In the way I'm doing it I get the fraction of trees predicting each change value (from 0 to 9) but all the trees predicting 10 or more changes are included in the same category (10+) Is there any way to tell the program to output the information on the full distribution? Many thanks in advance, Ana Ana Mar?a Millanes Romero Departamental 1 DI-210 Departamento de Biolog?a y Geolog?a (ESCET) Universidad Rey Juan Carlos C/ Tulip?n, s/n E-28933 M?stoles, Madrid Phone: (+34) 914888290 E-mail: ana.millanes at urjc.es From jschulte at clarkson.edu Mon Feb 8 13:43:47 2010 From: jschulte at clarkson.edu (James Schulte) Date: Mon, 8 Feb 2010 16:43:47 -0500 Subject: [Mesquitelist] PDAP t-test: t-values In-Reply-To: References: Message-ID: Dear Mesquite, I have a student working on a dataset trying to correlate two continuous variables. After calculating the positivized contrasts and plotting them against one another, we get a t-value on the order of 12.13 which is significant for these data. However, when the positivized values are exported to Origin 8 and a t-test is performed the t-value is only on the order of ~1.6. Does the t-value seem high in Mesquite or am I completely missing something in my evaluation of the t-test in PDAP? Thank you for any help and the file is attached. Cheers, Jim -------------- next part -------------- A non-text attachment was scrubbed... Name: LangenMesquiteFINAL.nex Type: application/octet-stream Size: 21585 bytes Desc: not available Url : http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100208/1c9d9c38/attachment-0001.obj -------------- next part -------------- James A. Schulte, II Department of Biology 177 Clarkson Science Center, MRC 5805 8 Clarkson Avenue Clarkson University Potsdam, NY 13699-5805 Phone: 315-268-4401 Fax: 315-268-7118 From peteremidford at yahoo.com Mon Feb 8 14:24:54 2010 From: peteremidford at yahoo.com (Peter E. Midford) Date: Mon, 8 Feb 2010 17:24:54 -0500 Subject: [Mesquitelist] PDAP t-test: t-values In-Reply-To: References: Message-ID: <56637971-FAAC-40A4-BBAE-C0E5E8A1F7D2@yahoo.com> Hi James, I'm Peter Midford, the maintainer of the PDAP package. I looked at your example and I agree that the t-statistic is rather large, but given the number of contrasts (43) and the reported r-squared and pearson correlation, the t-statistic looks right. Could you send me the values (whatever you've got) out of Origin as it might help me figure out where the problem is. Also, how exactly did you get the values that you put into Origin - there are different ways you could have gotten numbers out of Mesquite, and some methods tend to cause problems. Cheers, Peter On Feb 8, 2010, at 16:43, James Schulte wrote: > Dear Mesquite, > > I have a student working on a dataset trying to correlate two continuous variables. After calculating the positivized contrasts and plotting them against one another, we get a t-value on the order of 12.13 which is significant for these data. However, when the positivized values are exported to Origin 8 and a t-test is performed the t-value is only on the order of ~1.6. Does the t-value seem high in Mesquite or am I completely missing something in my evaluation of the t-test in PDAP? > > Thank you for any help and the file is attached. > > Cheers, > Jim > > > > James A. Schulte, II > Department of Biology > 177 Clarkson Science Center, MRC 5805 > 8 Clarkson Avenue > Clarkson University > Potsdam, NY 13699-5805 > Phone: 315-268-4401 > Fax: 315-268-7118_______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist -- Peter Midford Mesquite Developer From emad_sara at ymail.com Mon Feb 15 03:01:51 2010 From: emad_sara at ymail.com (Sara Emad) Date: Mon, 15 Feb 2010 03:01:51 -0800 (PST) Subject: [Mesquitelist] differentiation between mesquite and DIVA Message-ID: <626001.84278.qm@web113905.mail.gq1.yahoo.com> Dear All, I used mesquite and DIVA to reconstract the distribution range of nodes?for my data set?. In some cases I have different results (according to both of them are pasimony-based method). I would like to know the differentiation between these two programs. I guess the differrentiation is due to in Mesquite none of the biogeographical events (vicariance, dispersal, etc.) have any cost, although vicariance is the null model in DIVA. I am right? ? Thanks Sara ? ?Any help is appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100215/f4ffb845/attachment.html From flayamamoto at gmail.com Mon Feb 22 06:25:28 2010 From: flayamamoto at gmail.com (=?ISO-8859-1?Q?Fl=E1vio_Uemori_Yamamoto?=) Date: Mon, 22 Feb 2010 11:25:28 -0300 Subject: [Mesquitelist] Mesquite 2.72 , Kubuntu 9.04 and Sun Java 6. Message-ID: <9674ce851002220625g3368e3b3h50cfa8abd94da971@mail.gmail.com> Hello. This is my first e-mail to this list. I was using Mesquite version 2.6 (everything ok) and recently upgraded to version 2.72. Now, when I start the program, it opens a "crash" box with the message below: "There has been a problem starting a module (class java.lang.NoSuchFieldError). This may be the result of an old, incompatible package being used, or part of Mesquite was accidentally deleted. (module: Defaults; arguments: null; module being started: mesquite.minimal.Defaults.Defaults; ERROR: storedAsDefault; error class class java.lang.NoSuchFieldError [2])" My computer runs Linux Kubuntu 9.04 and has the java package "Sun Java(TM) Runtime Environment (JRE) 6". What am I doing wrong? Thank you. Best regards. Fl?vio Uemori Yamamoto Laborat?rio de Artr?podes, Instituto Butantan Av. Vital Brasil, 1500 05503-900 - S?o Paulo - SP - Brazil Telefone: 005511 3726-7222 ramal: 2235, 2180 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100222/87610fe5/attachment.html From patiny.s at gmail.com Wed Feb 24 13:51:38 2010 From: patiny.s at gmail.com (=?ISO-8859-1?Q?S=E9bastien_Patiny?=) Date: Wed, 24 Feb 2010 22:51:38 +0100 Subject: [Mesquitelist] Simple question Message-ID: <686090a71002241351h12448418mb4efa295aa100fbe@mail.gmail.com> Hi all, What are the taxon and character limits in Mesquite? Best, Seb -- ---------------------------------------------------- Dr S?bastien Patiny (Entomologist) Chemcom s.a. 1070 Brussels BELGIUM url : http://sites.google.com/site/patinys/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100224/0425f245/attachment.html From biodiverky at gmail.com Wed Feb 24 18:46:59 2010 From: biodiverky at gmail.com (Yi Kong) Date: Thu, 25 Feb 2010 10:46:59 +0800 Subject: [Mesquitelist] numbers of MPRs Message-ID: <57d1a1d51002241846k1b4ab98av9c2a957a13098a95@mail.gmail.com> Hi everybody, I meet an problem in parsimony reconstruction when I click *Summaries State Changes over trees,* this dialog box appears, "Number of MPRs exceeds that allowed - calculations can not be completed." Who can tell me how to reslove it? Thanks a lot! -- Yi Kong P.O. BOX159 No.1 Wenyuan road, College of Life Science, Nanjing Normal University, Nanjing, Jiangsu province 210046, P.R. China -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100225/746006ed/attachment.html From wangli at cshl.edu Thu Feb 25 08:27:05 2010 From: wangli at cshl.edu (Liya Wang) Date: Thu, 25 Feb 2010 11:27:05 -0500 Subject: [Mesquitelist] Manual for headless version of Mesquite Message-ID: <8f7b46211002250827n9f1d7b0td3ab3ae02d617a96@mail.gmail.com> Hello everybody, I am trying to use the headless version of Mesquite to do ancestral state reconstruction. However I feel it is not easy without a manual or tutorial. Does anyone know about the manual? Thanks, Liya -- Liya Wang, Ph.D. Cold Spring Harbor Laboratory Phone: 516 367-8404 Fax: 516 367-6851 From alej.c.s at gmail.com Thu Feb 25 12:13:28 2010 From: alej.c.s at gmail.com (Alejo C.S.) Date: Thu, 25 Feb 2010 17:13:28 -0300 Subject: [Mesquitelist] crash Xorg during Mesquite starts Message-ID: <86bb4e3b1002251213o74d2d6e1x20b6a970b82472ed@mail.gmail.com> Dear all, I'm using Mesquite 2.72 on Debian Squeeze (amd64) and Sun Java 1.6.0_18 in KDE 4.3.4 desktop environment. When the program is starting, suddenly my xserver (Xorg) crash and restarts from login screen. Nothing appears in the logs (system.log, Xorg.log, kdm.log). The odd thing is when using OpenJDK Runtime Environment (IcedTea6 1.7) (6b17-1.7-1) Mesquite starts perfect, but the functionality is awful. I've redirected the console output in the moment I run Mesquite to txt file, here is the point where all crash: Principal Authors: Wayne Maddison & David Maddison > Development Team: Wayne Maddison, David Maddison, Peter Midford, Jeff > Oliver > Development Team Alumnus: Danny Mandel > > Thu Feb 25 16:54:34 ART 2010 > Running under Java 1.6.0_18; virtual machine by Sun Microsystems Inc. on > Linux 2.6.32-trunk-amd64 (architecture: amd64) > User: marmokh > > Incorporated from /home/marmokh/Programas/Mesquite_Folder/./ > dom4j-1.6.1.jar iText.jar commons-logging-1.1.1.jar JSci.zip > commons-lang-2.3.jar commons-codec-1.3.jar Jama-1.0.1.zip pal.zip > commons-httpclient-3.1.jar > > Mesquite directory: /home/marmokh/Programas/Mesquite_Folder/./ > Log file located in: /home/marmokh/Mesquite_Support_Files > Prefs directory: /home/marmokh/Mesquite_Support_Files/Mesquite_Prefs > > Modules loading from directory > /home/marmokh/Programas/Mesquite_Folder/./mesquite/ > > ancstates basic categ charMatrices charts cont genesis io lists minimal > parsimony stochchar trees align assoc batchArch > It seems that after loading the package batchArch the system crash. One thing that I'm very confused is that in my home computer I have the same system (Debian amd64 Squeeze and KDE4) and mesquite runs just fine with sun JAVA. My home computer works with a nvidia video card and my work computer (where is the problem) runs a intel video card, maybe that is the problem????. Thanks in advance. Alejo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100225/6c1c7448/attachment.html From v_candida at hotmail.com Fri Feb 26 10:22:04 2010 From: v_candida at hotmail.com (m. candida) Date: Fri, 26 Feb 2010 18:22:04 +0000 Subject: [Mesquitelist] importing tree for matrix Message-ID: I have a matrix with X taxa. In order to run IC tests for the characters I need to import a tree. So, two questions: 1. How can I import a tree so that it is associated with my matrix? 2. Do I need to manually clip those taxa from the tree that are not in my matrix? Any advice would be appreciated. Eric _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20100226/f176b80a/attachment.html From sylvain at bergianska.se Fri Feb 26 10:45:27 2010 From: sylvain at bergianska.se (sylvain at bergianska.se) Date: Fri, 26 Feb 2010 19:45:27 +0100 Subject: [Mesquitelist] Request In-Reply-To: References: Message-ID: <50ada8cace1dc8d88b8e3e795b15c5a7.squirrel@www.bergianska.se> Dear Sir or Madam, Please, remove my email address from this mailinglist. Thank you! Sylvain