From wollenbergk at niaid.nih.gov Fri Aug 4 07:52:27 2006 From: wollenbergk at niaid.nih.gov (Kurt Wollenberg) Date: Fri Aug 4 07:52:37 2006 Subject: [Mesquitelist] Error parsing tree from file In-Reply-To: Message-ID: Hello all: I am just starting to use Mesquite and have run up against a problem I haven't been able to solve. I have two DNA sequence data sets for which I have consensus trees from MrBayes (from the MrBayes .con files). The character data read into Mesquite just fine. When I read my trees into their respective tree windows one parses just fine while the other throws up a "read clade failed" error. I've checked the tree labels and they exactly match the character matrix labels. I've parsed the Newick tree by hand and can't find any mismatched commas, colons, or parentheses. My hand-parsed tree matches the tree in my MrBayes.out file, so it appears that I manually parsed it correctly. I've cut and pasted the tree descriptions (from the initial parenthesis to the final one) from one file to the other and vice versa and I get the same error for the bad tree in the good file (so I'm pretty certain I haven't introduced any hidden characters into the file). Below is the offending tree file. Any ideas from the Mesquite community on how to resolve this would be greatly appreciated. #NEXUS [ID: 2247068928] begin trees; [Note: This tree contains information on the topology, branch lengths (if present), and the probability of the partition indicated by the branch.] TREE con_50_majrule = (SIV_mac:0.223786,((SIVrd_10:0.086977,268a_30:0.018678,268a_31:0.049755,268a _37:0.027715,(((268b_21:0.053170,268b_50:0.014379)0.88:0.034542,268c_29:0.05 2608)1.00:0.112200,268b_25:0.026808,(268c_50:0.016847,268c_55:0.020524,268c_ 69:0.033555)1.00:0.110310)0.67:0.051291,268b_22:0.031063,268c_61:0.018438)0. 97:0.095072,SIVrd_27:0.041917,(268c_11:0.013826,268c_15:0.051460)1.00:0.1045 18)0.78:0.054720,(((SIVrd_1:0.009825,SIVrd_19:0.017794,268a_24:0.009122,268a _29:0.027071,(268b_27:0.020091,268b_53:0.019831)0.98:0.038113)0.86:0.044486, (SIVrd_7:0.053240,SIVrd_18:0.090587)0.63:0.054170,(SIVrd_16:0.144389,SIVrd_1 7:0.067918,SIV_K6W:0.126133)0.98:0.058607,SIVrd_21:0.085361,(268b_44:0.03615 3,268b_46:0.011236)1.00:0.116152)0.54:0.056903,(268a_26:0.006329,268a_34:0.0 07299)1.00:0.180776)0.54:0.049342); [second tree cut to save space] end; Cheers, Kurt Wollenberg, Ph.D. Phylogenetics and Sequence Analysis Consultant Biocomputing Research Consulting Section Bioinformatics and Scientific IT Program (BSIP) NIH/NIAID/OTIS Contractor, MSD Inc. Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From wmaddisn at interchange.ubc.ca Fri Aug 4 17:14:42 2006 From: wmaddisn at interchange.ubc.ca (Wayne Maddison) Date: Fri Aug 4 17:14:39 2006 Subject: [Mesquitelist] Error parsing tree from file In-Reply-To: References: Message-ID: I created a taxa block with the taxa names as implied by your tree, and inserted it into the file, and then read the file. Mesquite read your tree just fine. (I removed the line breaks which I presume were inserted by your email program). I'll send you the file I worked from off-list to see if it works for you, so we can understand what's going wrong with your files. Wayne At 10:52 AM -0400 4.8.2006, Kurt Wollenberg wrote: >Hello all: > >I am just starting to use Mesquite and have run up against a problem I >haven't been able to solve. I have two DNA sequence data sets for which I >have consensus trees from MrBayes (from the MrBayes .con files). The >character data read into Mesquite just fine. When I read my trees into their >respective tree windows one parses just fine while the other throws up a >"read clade failed" error. I've checked the tree labels and they exactly >match the character matrix labels. I've parsed the Newick tree by hand and >can't find any mismatched commas, colons, or parentheses. My hand-parsed >tree matches the tree in my MrBayes.out file, so it appears that I manually >parsed it correctly. I've cut and pasted the tree descriptions (from the >initial parenthesis to the final one) from one file to the other and vice >versa and I get the same error for the bad tree in the good file (so I'm >pretty certain I haven't introduced any hidden characters into the file). >Below is the offending tree file. Any ideas from the Mesquite community on >how to resolve this would be greatly appreciated. > >#NEXUS > >[ID: 2247068928] >begin trees; > [Note: This tree contains information on the topology, > branch lengths (if present), and the probability > of the partition indicated by the branch.] > TREE con_50_majrule = >(SIV_mac:0.223786,((SIVrd_10:0.086977,268a_30:0.018678,268a_31:0.049755,268a >_37:0.027715,(((268b_21:0.053170,268b_50:0.014379)0.88:0.034542,268c_29:0.05 >2608)1.00:0.112200,268b_25:0.026808,(268c_50:0.016847,268c_55:0.020524,268c_ >69:0.033555)1.00:0.110310)0.67:0.051291,268b_22:0.031063,268c_61:0.018438)0. >97:0.095072,SIVrd_27:0.041917,(268c_11:0.013826,268c_15:0.051460)1.00:0.1045 >18)0.78:0.054720,(((SIVrd_1:0.009825,SIVrd_19:0.017794,268a_24:0.009122,268a >_29:0.027071,(268b_27:0.020091,268b_53:0.019831)0.98:0.038113)0.86:0.044486, >(SIVrd_7:0.053240,SIVrd_18:0.090587)0.63:0.054170,(SIVrd_16:0.144389,SIVrd_1 >7:0.067918,SIV_K6W:0.126133)0.98:0.058607,SIVrd_21:0.085361,(268b_44:0.03615 >3,268b_46:0.011236)1.00:0.116152)0.54:0.056903,(268a_26:0.006329,268a_34:0.0 >07299)1.00:0.180776)0.54:0.049342); > >[second tree cut to save space] >end; > >Cheers, >Kurt Wollenberg, Ph.D. >Phylogenetics and Sequence Analysis Consultant >Biocomputing Research Consulting Section >Bioinformatics and Scientific IT Program (BSIP) >NIH/NIAID/OTIS >Contractor, MSD Inc. > >Disclaimer: >The information in this e-mail and any of its attachments is confidential >and may contain sensitive information. It should not be used by anyone who >is not the original intended recipient. If you have received this e-mail in >error please inform the sender and delete it from your mailbox or any other >storage devices. National Institute of Allergy and Infectious Diseases shall >not accept liability for any statements made that are sender's own and not >expressly made on behalf of the NIAID by one of its representatives. > >_______________________________________________ >Mesquitelist mailing list >Mesquitelist@mesquiteproject.org >http://mesquiteproject.org/mailman/listinfo/mesquitelist -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Departments of Zoology and Botany and Centre for Biodiversity Research 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wmaddisn@interchange.ubc.ca FAX: (604) 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org CIPRes: http://www.phylo.org Home page: http://salticidae.org/wpm/home.html