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Simultaneous multiple alignment and phylogeny estimation

• Goals
  • · design of new methods for simultaneous estimation of alignments and trees
  • · implementation of simulator tools for evolution which produce more realistic data
  • · educational outreach


• Publications
  • Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
    Science '09: Liu, Raghavan, Nelesen, Linder, & Warnow
    
  
  
  • Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
    TCBB '09: Liu, Nelesen, Raghavan, Linder, & Warnow
    
  
  
  • The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analyses
    PSB '08: Nelesen, Liu, Zhao, Linder, & Warnow
    

Supertree methods for combining phylogenies

• Goals
  • · design of fast and scalable supertree methods
  • · distribution of usable software to the research community


• Publications
  • A Simulation Study Comparing Supertree and Combined Analysis Methods using SMIDGen
    WABI '09: Swenson, Barbançon, Linder, & Warnow
    

Fast techniques for maximum likelihood and maximum parsimony

• Goals
  • · design of new methods capable of approximating MP on thousands of sequences in reasonable time periods


• Publications
  • Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees
    CSB '04: Roshan, Moret, Warnow, & Williams