From stevet from bio.fsu.edu Fri Mar 21 07:45:03 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Fri Mar 21 09:19:14 2008 Subject: [Molecular-evolution] GCG/SeqLab petition Message-ID: <20080321083045.G1788@epsilon.bio.fsu.edu> Hi all - I apologize for my multiple cross-group postings but I feel the importance and urgency of this message warrant it. As many of you are aware, last summer Accelrys announced that they would be discontinuing support for GCG and SeqLab this upcoming June. That situation dismayed me and others and I wanted to do something about it. I contacted Steven Smith, one of the original authors of SeqLab, and discussed the situation with him. He volunteered to contact Accelrys in an attempt to minimally get SeqLab's license and code released to him. I gave Steve several months to try to persuade the company. Accelrys was not very cooperative. Therefore, I set about creating a petition in an attempt to add some leverage. I've contacted a few of you earlier regarding this initiative and appreciate your support. Anyway, I have created and posted that petition. It's at: http://www.petitiononline.com/gcg/petition.html And a nicely formatted PDF version is available in my own Web space: http://bio.fsu.edu/~stevet/Accelrys_petition.pdf I would very much appreciate you adding your name to this petition, if you agree with our sentiment. Thank you for your time! Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From clements from nescent.org Mon Mar 24 15:32:48 2008 From: clements from nescent.org (Dave Clements) Date: Tue Mar 25 09:53:59 2008 Subject: [Molecular-evolution] GMOD Summer School, July 11-13, 2008, Durham, NC, USA Message-ID: GMOD Summer School 11-13 July, 2008 National Evolutionary Synthesis Center (NESCent) Durham, North Carolina, USA The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will be held July 11-13, 2008 at the National Evolutionary Synthesis Center (NESCent), in Durham, North Carolina, USA. GMOD is a collection of interoperable open source software components for managing genomic data. GMOD components are used in diverse contexts, with both emerging and established model organisms. The course will provide an overview of GMOD and cover these popular components in detail: * Chado - a modular and extensible database schema * Apollo - genome annotation editor * GBrowse - genome viewer * CMap - comparative map viewer * Community Annotation System - GMOD's most popular components in a single system This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to use GMOD. The National Evolutionary Synthesis Center (NESCent, http://nescent.org) has joined the GMOD project with the goal of lowering the barrier to entry for research communities focused on emerging model organisms. The GMOD Summer School is a part of this effort. NESCent is also extending GMOD components, particularly Chado, to better support comparative and evolutionary data. If you are interested in attending the GMOD Summer School please submit a Statement of Interest before April 15, 2008. The course is free but enrollment is limited. For application information and a tentative program see: http://gmod.org/GMOD_Summer_School Please let me know if you have any questions, comments, or requests. Thanks, Dave Clements GMOD Help Desk help@gmod.org ------------------------ NESCent offers various courses and workshops, as well as funding post-doctoral and sabbatical positions, working groups and other meetings. For more information about research and training opportunities at NESCent, visit our website at www.nescent.org. Sign up for our quarterly electronic newsletter at http://www.nescent.org/about/contact.php to automatically receive information about events at NESCent. From trondaun from nt.ntnu.no Tue Mar 25 16:18:57 2008 From: trondaun from nt.ntnu.no (Trond Erik Vee Aune) Date: Tue Mar 25 16:21:38 2008 Subject: [Molecular-evolution] Help with phylogenetic tree construction Message-ID: Hi, What I would like to to is to generate a phylogenetic tree based on 16s sequences from 30 different bacteria plotted onto a larger tree showing selected organisms from different prominent phyla. The idea is to display the relationship between my 30 organisms AND how they relate to the rest of the prokaryotes. I used to this sort of thing by downloading each sequence from NCBI and then align them and generate a phylogenetic tree in ClustalW or some other software. I hope there exist some internet tools now that can do it all for me, i.e. that I just select the species/strains and the software retrives the sequences, aligns them and creates the tree according to mye criteria. Do you know of any such sequences or do people still do these kind of things "by hand"? Regards, Trond Erik