From PSJARRIN at puce.edu.ec Mon Jul 6 13:44:00 2009 From: PSJARRIN at puce.edu.ec (JARRIN VALLADARES PABLO SANTIAGO) Date: Mon, 6 Jul 2009 15:44:00 -0500 Subject: [Mesquitelist] Assigning Group IDs Message-ID: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090706/e7d3091f/attachment.html From samd at seas.upenn.edu Tue Jul 7 11:57:41 2009 From: samd at seas.upenn.edu (Sam Donnelly) Date: Tue, 07 Jul 2009 14:57:41 -0400 Subject: [Mesquitelist] NEXUS file -> CategoricalData Message-ID: <4A539AA5.7030706@seas.upenn.edu> Hello, What's the best way to programmatically get a CategoricalData object given a Nexus file? In other words, I'm looking for some way to go: here's a Nexus file, give me a CategoricalData object that represents that file. Thanks so much! Sam From twidhelm at gmail.com Tue Jul 7 14:02:07 2009 From: twidhelm at gmail.com (Todd Widhelm) Date: Tue, 7 Jul 2009 16:02:07 -0500 Subject: [Mesquitelist] Converting amino acids to nucleotides Message-ID: <40C2B72D-12AB-4916-9912-7777F4EC4060@gmail.com> I have converted a nucleotide sequence matrix to an amino acid sequence (Translate DNA to Protein). I then aligned the amino acid sequences. I cannot figure out how to convert amino acid sequences back into nucleotide sequences. Could you please help me? Thanks, Todd Widhelm The Field Museum University of Illinois at Chicago phone: (402) 210-8046 http://www2.uic.edu/~twidhe2/Todd_site/Home.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090707/f0d39ee1/attachment.html From kipwill at berkeley.edu Tue Jul 7 14:50:46 2009 From: kipwill at berkeley.edu (Kipling (Kip) Will) Date: Tue, 07 Jul 2009 14:50:46 -0700 Subject: [Mesquitelist] Assigning Group IDs In-Reply-To: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> References: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> Message-ID: <4A53C336.1040703@berkeley.edu> You can edit the nexus file directly in a plain text editor, e.g. BEGIN SETS; TAXPARTITION * UNTITLED = In_Group : 1- 146: Out_Group : 120 - 147; CHARPARTITION * UNTITLED = Head : 1 - 11, Thorax ; END; k. JARRIN VALLADARES PABLO SANTIAGO wrote: > 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 -- Kipling W. Will Associate Professor/Insect Systematist Associate Director,Essig Museum of Entomology mail to: 137 Mulford Hall ESPM Dept.- Organisms & Environment Div. University of California Berkeley, California 94720 phone 510-642-4296 fax 510-643-5438 From kipwill at berkeley.edu Tue Jul 7 14:56:28 2009 From: kipwill at berkeley.edu (Kipling (Kip) Will) Date: Tue, 07 Jul 2009 14:56:28 -0700 Subject: [Mesquitelist] Assigning Group IDs In-Reply-To: <4A53C336.1040703@berkeley.edu> References: <90EE5EB4DA6D164893805886A51F3BD708AA85A6@PUCEMAIL.puce.edu.ec> <4A53C336.1040703@berkeley.edu> Message-ID: <4A53C48C.8000303@berkeley.edu> Sorry the number were scrambled in my previous example. This will make more sense.. BEGIN SETS; TAXPARTITION * UNTITLED = In_Group : 1- 119: Out_Group : 120 - 147; CHARPARTITION * UNTITLED = Head : 1 - 11, Thorax : 12 - 38, ; END; -- Kipling W. Will Associate Professor/Insect Systematist Associate Director,Essig Museum of Entomology mail to: 137 Mulford Hall ESPM Dept.- Organisms & Environment Div. University of California Berkeley, California 94720 phone 510-642-4296 fax 510-643-5438 From capy243 at gmail.com Tue Jul 7 15:06:59 2009 From: capy243 at gmail.com (Cassia Oliveira) Date: Tue, 7 Jul 2009 17:06:59 -0500 Subject: [Mesquitelist] Phylogenetic Correlation Message-ID: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> How can I use mesquite to calculate phylogenetic signal using continuous characters? Thanks, Capy. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090707/102f06ba/attachment.html From peteremidford at yahoo.com Tue Jul 7 15:56:46 2009 From: peteremidford at yahoo.com (Peter E. Midford) Date: Tue, 7 Jul 2009 17:56:46 -0500 Subject: [Mesquitelist] Phylogenetic Correlation In-Reply-To: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> References: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> Message-ID: <71D9FADA-A753-4C1F-B750-1C6BE1D20739@yahoo.com> Can you clarify - are you testing for phylogenetic signal or trying to calculate a phylogenetically corrected correlation between characters? Peter On Jul 7, 2009, at 17:06, Cassia Oliveira wrote: > How can I use mesquite to calculate phylogenetic signal using > continuous characters? > Thanks, > Capy. > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist -- Peter Midford Mesquite Developer From capy243 at gmail.com Tue Jul 7 20:01:20 2009 From: capy243 at gmail.com (Cassia Oliveira) Date: Tue, 7 Jul 2009 22:01:20 -0500 Subject: [Mesquitelist] Phylogenetic Correlation In-Reply-To: <71D9FADA-A753-4C1F-B750-1C6BE1D20739@yahoo.com> References: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> <71D9FADA-A753-4C1F-B750-1C6BE1D20739@yahoo.com> Message-ID: <443bdb5b0907072001v6a18aeeal4fa7a9b3250a7d7f@mail.gmail.com> Hi Peter, I'm testing for phylogenetic signal. I'm trying to find if there is a positive correlation between cuticular hydrocarbons and the phylogeny for the species I'm studying. I know that once I trace the characters onto the phylogeny using trace character history I can reshuffle the data to generate a random distribution of values. I can then obtain the p value by counting the number of reshuffled datasets with fewer changes than the empirical data and dividing this by the number of times I reshuffled the data. This approach works fine with categorical data, but not with continuous data. I did calculate phylogenetic signal using the test for serial independence using Phylogenetic Independence software by Reeve and Abouheif (2003). However, I spent a lot of time to learn how to use mesquite and so would like to get the results from it as well. Any suggestions? Thank you! Cassia. On Tue, Jul 7, 2009 at 5:56 PM, Peter E. Midford wrote: > Can you clarify - are you testing for phylogenetic signal or trying to > calculate a phylogenetically corrected correlation between characters? > > Peter > > > On Jul 7, 2009, at 17:06, Cassia Oliveira wrote: > > How can I use mesquite to calculate phylogenetic signal using continuous >> characters? >> Thanks, >> Capy. >> _______________________________________________ >> Mesquitelist mailing list >> Mesquitelist at mesquiteproject.org >> http://mesquiteproject.org/mailman/listinfo/mesquitelist >> > > -- > Peter Midford > Mesquite Developer > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090707/6bbf98ab/attachment.html From michel.laurin at upmc.fr Tue Jul 7 23:11:29 2009 From: michel.laurin at upmc.fr (Michel LAURIN) Date: Wed, 08 Jul 2009 08:11:29 +0200 Subject: [Mesquitelist] Phylogenetic Correlation In-Reply-To: <443bdb5b0907072001v6a18aeeal4fa7a9b3250a7d7f@mail.gmail.com> References: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> <71D9FADA-A753-4C1F-B750-1C6BE1D20739@yahoo.com> <443bdb5b0907072001v6a18aeeal4fa7a9b3250a7d7f@mail.gmail.com> Message-ID: <20090708081129.hkmedmh3wwoso4wo@courriel.upmc.fr> Hello Cassia, To detect a phylogenetic signal in continuous characters using Mesquite, you can compare the squared length of a character (or of a whole matrix of characters) to the squared length of randomized trees. However, since the squared length depends on branch lengths, you cannot use random tree generation algorithms that modify these, so the easiest way is to permute the position of the taxa randomly onto the tree. The earliest use of this method that I am aware of is in this paper, which I can send as a pdf file, if you want: Laurin, M. 2004. The evolution of body size, Cope's rule and the origin of amniotes. Syst. Biol. 53:594-622. I am not sure why you think that this does not work for continuous characters. Note that you can get a histogram of distribution for many (e.g. 100000) randomized trees in a single step. A more sophisticated method is available in PDAP (DOS version), but it has not been implemented in Mesquite yet. It is described in: Blomberg, S. P., T. J. Garland, and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745. You can download the paper from Ted Garland's page, or e-mail me for it (I have the pdf). Note that to establish character correlation, you could have used the PDAP:PDTREE module for mesquite, which computes phylogenetically independent contrasts and has the great interface (GUI) that Mesquite has. Cheers, Michel Quoting Cassia Oliveira : > Hi Peter, > > I'm testing for phylogenetic signal. I'm trying to find if there is a > positive correlation between cuticular hydrocarbons and the phylogeny for > the species I'm studying. I know that once I trace the characters onto the > phylogeny using trace character history I can reshuffle the data to generate > a random distribution of values. I can then obtain the p value by counting > the number of reshuffled datasets with fewer changes than the empirical data > and dividing this by the number of times I reshuffled the data. This > approach works fine with categorical data, but not with continuous data. I > did calculate phylogenetic signal using the test for serial independence > using Phylogenetic Independence software by Reeve and Abouheif (2003). > However, I spent a lot of time to learn how to use mesquite and so would > like to get the results from it as well. Any suggestions? > > Thank you! > > Cassia. > > > On Tue, Jul 7, 2009 at 5:56 PM, Peter E. Midford > wrote: > >> Can you clarify - are you testing for phylogenetic signal or trying to >> calculate a phylogenetically corrected correlation between characters? >> >> Peter >> >> >> On Jul 7, 2009, at 17:06, Cassia Oliveira wrote: >> >> How can I use mesquite to calculate phylogenetic signal using continuous >>> characters? >>> Thanks, >>> Capy. >>> _______________________________________________ >>> Mesquitelist mailing list >>> Mesquitelist at mesquiteproject.org >>> http://mesquiteproject.org/mailman/listinfo/mesquitelist >>> >> >> -- >> Peter Midford >> Mesquite Developer >> >> >> >> > From mcmirande at gmail.com Wed Jul 8 07:00:03 2009 From: mcmirande at gmail.com (Marcos Mirande) Date: Wed, 8 Jul 2009 11:00:03 -0300 Subject: [Mesquitelist] Phylogenetic Correlation In-Reply-To: <20090708081129.hkmedmh3wwoso4wo@courriel.upmc.fr> References: <443bdb5b0907071506y35118638i5bffb676851a2be@mail.gmail.com> <71D9FADA-A753-4C1F-B750-1C6BE1D20739@yahoo.com> <443bdb5b0907072001v6a18aeeal4fa7a9b3250a7d7f@mail.gmail.com> <20090708081129.hkmedmh3wwoso4wo@courriel.upmc.fr> Message-ID: ... well, actually the best way to detect phylogenetic signal in continuous characters is not using Mesquite... but using TNT... Just add them to a discrete-characters matrix, and analyze it... As this is a Mesquite forum, I'll not profundize on that, but if somebody is interested in this issue, please let me know (or visit the TNT wiki page: tnt.insectmuseum.org ) Cheers, Marcos 2009/7/8, Michel LAURIN : > Hello Cassia, > > To detect a phylogenetic signal in continuous characters using > Mesquite, you can compare the squared length of a character (or of a > whole matrix of characters) to the squared length of randomized trees. > However, since the squared length depends on branch lengths, you > cannot use random tree generation algorithms that modify these, so the > easiest way is to permute the position of the taxa randomly onto the > tree. The earliest use of this method that I am aware of is in this > paper, which I can send as a pdf file, if you want: > > Laurin, M. 2004. The evolution of body size, Cope's rule and the > origin of amniotes. Syst. Biol. 53:594-622. > > I am not sure why you think that this does not work for continuous > characters. Note that you can get a histogram of distribution for many > (e.g. 100000) randomized trees in a single step. > > A more sophisticated method is available in PDAP (DOS > version), but it has not been implemented in Mesquite yet. It is > described in: > > Blomberg, S. P., T. J. Garland, and A. R. Ives. 2003. Testing for > phylogenetic signal in comparative data: behavioral traits are more > labile. Evolution 57:717-745. > > You can download the paper from Ted Garland's page, or e-mail me for > it (I have the pdf). > > Note that to establish character correlation, you could have used the > PDAP:PDTREE module for mesquite, which computes phylogenetically > independent contrasts and has the great interface (GUI) that Mesquite > has. > > Cheers, > > Michel > > > Quoting Cassia Oliveira : > >> Hi Peter, >> >> I'm testing for phylogenetic signal. I'm trying to find if there is a >> positive correlation between cuticular hydrocarbons and the phylogeny for >> the species I'm studying. I know that once I trace the characters onto the >> phylogeny using trace character history I can reshuffle the data to >> generate >> a random distribution of values. I can then obtain the p value by counting >> the number of reshuffled datasets with fewer changes than the empirical >> data >> and dividing this by the number of times I reshuffled the data. This >> approach works fine with categorical data, but not with continuous data. I >> did calculate phylogenetic signal using the test for serial independence >> using Phylogenetic Independence software by Reeve and Abouheif (2003). >> However, I spent a lot of time to learn how to use mesquite and so would >> like to get the results from it as well. Any suggestions? >> >> Thank you! >> >> Cassia. >> >> >> On Tue, Jul 7, 2009 at 5:56 PM, Peter E. Midford >> wrote: >> >>> Can you clarify - are you testing for phylogenetic signal or trying to >>> calculate a phylogenetically corrected correlation between characters? >>> >>> Peter >>> >>> >>> On Jul 7, 2009, at 17:06, Cassia Oliveira wrote: >>> >>> How can I use mesquite to calculate phylogenetic signal using >>> continuous >>>> characters? >>>> Thanks, >>>> Capy. >>>> _______________________________________________ >>>> Mesquitelist mailing list >>>> Mesquitelist at mesquiteproject.org >>>> http://mesquiteproject.org/mailman/listinfo/mesquitelist >>>> >>> >>> -- >>> Peter Midford >>> Mesquite Developer >>> >>> >>> >>> >> > > > > _______________________________________________ > Mesquitelist mailing list > Mesquitelist at mesquiteproject.org > http://mesquiteproject.org/mailman/listinfo/mesquitelist > -- Juan Marcos Mirande Fundaci?n Miguel Lillo - CONICET Miguel Lillo 251 (4000) San Miguel de Tucum?n Argentina From twidhelm at gmail.com Wed Jul 8 08:50:14 2009 From: twidhelm at gmail.com (Todd Widhelm) Date: Wed, 8 Jul 2009 10:50:14 -0500 Subject: [Mesquitelist] Amino acid to nucleotide Message-ID: Hello friends, Does anyone know if it is possible to convert a protein sequence alignment into a nucleotide sequence alignment? I know how to translate DNA into a protein sequence. I do this to align amino acid sequences, then I convert them back to nucleotides for analysis. This can be done easily in Bioedit, but I do not like jumping back and forth from my mac to a pc. Please let me know if this is possible to do with Mesquite. Thanks, Todd Widhelm The Field Museum University of Illinois at Chicago phone: (402) 210-8046 http://www2.uic.edu/~twidhe2/Todd_site/Home.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20090708/20c044dd/attachment.html From jonah.choiniere at gmail.com Fri Jul 10 00:24:51 2009 From: jonah.choiniere at gmail.com (Jonah Choiniere) Date: Fri, 10 Jul 2009 15:24:51 +0800 Subject: [Mesquitelist] Generating all possible resolutions for a polytomy Message-ID: 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 From rrs at bumail.bradley.edu Wed Jul 15 08:30:54 2009 From: rrs at bumail.bradley.edu (Robert Stephens) Date: Wed, 15 Jul 2009 10:30:54 -0500 Subject: [Mesquitelist] Message-ID: rrs at bumail.bradley.edu