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iEvoBio_SplitDB

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iEvoBio 2011 Talk

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iEvoBio_SplitDB

  1. 1. A Mechanism for Storing, Retrieving and Evaluating Statistical Properties of PhylogeneticTrees<br />Haleh Ashki, James C. Wilgenbusch, and Paul van der Mark.<br />Department of Scientific Computing, Florida State University, Tallahassee, FL<br />
  2. 2. Motivation<br />
  3. 3. Causes of conflicting results:<br /><ul><li> Computational methods: (MCMC, Bayesian)
  4. 4. Models: (substitution models, free parameters calculated during stochastic methods )
  5. 5. Biological problem : (Gene Tree vs Species Tree)</li></li></ul><li>Solution<br />Developing a tool to identify conflicting result.<br /><ul><li> Store Data: Database: Better data retention; Speed ; Interoperability ; Fault tolerance.
  6. 6. Data Manipulate and Visualize: Tables, Plots, Tree views.</li></li></ul><li>Application<br />Core:<br />Python:<br />Dendropy(Sukumaran, J. and Mark T. Holder. 2010 )<br />MySQLdb(http://mysql-python.sourceforge.net/MySQLdb.html)<br />Matplotlib(http://matplotlib.sourceforge.net/)<br />Database:<br />MySQL 5.0 (Running on Linux Server)<br />Web User Interface:<br />Joomla: CMS & Application Framework<br />PHP, JavaScript, GoogleAPI<br />
  7. 7. Accept Nexus Tree files as Input From:<br />MrBayes(Huelsenbeck, J. P. and F. Ronquist. 2001 )<br />Paup(Swofford, D. L. )<br />RAxML(Stamatakis, A., Ludwig, T., and Meier, H. )<br />Garli(Zwickl,D.J.,2006.)<br />
  8. 8. Software<br />Available :<br />https://bpd.sc.fsu.edu/<br />The Sourceforge page:<br />http://sourceforge.net/projects/splitdb/<br />
  9. 9. Thanks To<br />Department of Scientific Computing, Florida State University.<br />The National Science Foundation for funding to support some of this work(EF-0849861)<br />
  10. 10. Demo<br />

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