Tandy Warnow

Summary

Affiliation: University of Texas
Country: USA

Publications

  1. pmc DACTAL: divide-and-conquer trees (almost) without alignments
    Serita Nelesen
    Department of Computer Science, Calvin College, Grand Rapids, MI 49546, USA
    Bioinformatics 28:i274-82. 2012
  2. pmc RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation
    Kevin Liu
    Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 6:e27731. 2011
  3. pmc Treelength optimization for phylogeny estimation
    Kevin Liu
    Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 7:e33104. 2012
  4. pmc MRL and SuperFine+MRL: new supertree methods
    Nam Nguyen
    Department of Computer Science, University of Texas at Austin, Austin, Texas, USA
    Algorithms Mol Biol 7:3. 2012
  5. pmc A simulation study comparing supertree and combined analysis methods using SMIDGen
    M Shel Swenson
    Department of Computer Sciences, The University of Texas at Austin, Austin TX, USA
    Algorithms Mol Biol 5:8. 2010
  6. doi Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    Kevin Liu
    Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA
    Science 324:1561-4. 2009
  7. doi Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy
    Kevin Liu
    The University of Texas at Austin, Austin, TX 78712, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:7-21. 2009
  8. doi SuperFine: fast and accurate supertree estimation
    M Shel Swenson
    Department of Computer Science, The University of Texas at Austin, Austin, TX, USA
    Syst Biol 61:214-27. 2012
  9. ncbi Phylogenetic networks: modeling, reconstructibility, and accuracy
    Bernard M E Moret
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:13-23. 2004
  10. pmc Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles
    Yun Yu
    Department of Computer Science, Rice University, Houston, Texas 77005, USA
    J Comput Biol 18:1543-59. 2011

Collaborators

Detail Information

Publications22

  1. pmc DACTAL: divide-and-conquer trees (almost) without alignments
    Serita Nelesen
    Department of Computer Science, Calvin College, Grand Rapids, MI 49546, USA
    Bioinformatics 28:i274-82. 2012
    ..While phylogenetic analyses of datasets containing 1000-5000 sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem of much greater complexity and scale...
  2. pmc RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation
    Kevin Liu
    Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 6:e27731. 2011
    ..Thus, our study shows that very large phylogenies can be estimated very quickly using FastTree, with little (and in some cases no) degradation in tree accuracy, as compared to RAxML...
  3. pmc Treelength optimization for phylogeny estimation
    Kevin Liu
    Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
    PLoS ONE 7:e33104. 2012
    ..These findings, taken as a whole, suggest that treelength optimization is not as good an approach to phylogenetic tree estimation as maximum likelihood based upon good alignment methods...
  4. pmc MRL and SuperFine+MRL: new supertree methods
    Nam Nguyen
    Department of Computer Science, University of Texas at Austin, Austin, Texas, USA
    Algorithms Mol Biol 7:3. 2012
    ..abstract:..
  5. pmc A simulation study comparing supertree and combined analysis methods using SMIDGen
    M Shel Swenson
    Department of Computer Sciences, The University of Texas at Austin, Austin TX, USA
    Algorithms Mol Biol 5:8. 2010
    ..The source tree and combined datasets used in this study can be used to test other supertree and combined analysis methods...
  6. doi Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    Kevin Liu
    Department of Computer Sciences, University of Texas at Austin, One University Station C0500, Austin, TX 78712, USA
    Science 324:1561-4. 2009
    ..In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies...
  7. doi Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy
    Kevin Liu
    The University of Texas at Austin, Austin, TX 78712, USA
    IEEE/ACM Trans Comput Biol Bioinform 6:7-21. 2009
    ..We also show that optimizing under this affine gap penalty produces trees whose topological accuracy is better than ClustalW+MP, and competitive with the current best two-phase methods...
  8. doi SuperFine: fast and accurate supertree estimation
    M Shel Swenson
    Department of Computer Science, The University of Texas at Austin, Austin, TX, USA
    Syst Biol 61:214-27. 2012
    ..Furthermore, SuperFine-boosted matrix representation with parsimony (MRP, the most well-known supertree method) approaches the accuracy of ML methods on supermatrix data sets under realistic conditions...
  9. ncbi Phylogenetic networks: modeling, reconstructibility, and accuracy
    Bernard M E Moret
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    IEEE/ACM Trans Comput Biol Bioinform 1:13-23. 2004
    ..Our results allow for the systematic study of existing network methods, and for the design of new accurate ones...
  10. pmc Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles
    Yun Yu
    Department of Computer Science, Rice University, Houston, Texas 77005, USA
    J Comput Biol 18:1543-59. 2011
    ..In addition, we devise MDC-based algorithms for cases when multiple alleles per species may be sampled. We study the performance of these methods in coalescent-based computer simulations...
  11. doi Large-scale multiple sequence alignment and tree estimation using SATé
    Kevin Liu
    Department of Computer Science, Rice University, Houston, TX, USA
    Methods Mol Biol 1079:219-44. 2014
    ..We also provide a discussion of how to modify these settings to obtain improved results, and how to use SATé in a phylogenetic analysis pipeline. ..
  12. doi Naive binning improves phylogenomic analyses
    Md Shamsuzzoha Bayzid
    Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
    Bioinformatics 29:2277-84. 2013
    ..Although many methods have been developed for this problem, little is understood about the relative performance of these methods when estimated gene trees are poorly estimated, owing to inadequate phylogenetic signal...
  13. doi Estimating optimal species trees from incomplete gene trees under deep coalescence
    Md Shamsuzzoha Bayzid
    Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA
    J Comput Biol 19:591-605. 2012
    ..The second most accurate method, MRP (a standard supertree method), can analyze very large datasets and produces very good trees, making MRP a potentially acceptable alternative to *BEAST for large datasets...
  14. doi FastSP: linear time calculation of alignment accuracy
    Siavash Mirarab
    Department of Computer Science, The University of Texas at Austin, Austin, TX 78701, USA
    Bioinformatics 27:3250-8. 2011
    ..However, the brute-force technique for calculating this set is quadratic in the input size. The remaining standard technique, Cline Shift Score, inherently requires quadratic time...
  15. ncbi Pattern identification in biogeography
    Ganeshkumar Ganapathy
    Department of Computer Sciences, The University of Texas at Austin, Austin, TX 78712, USA
    IEEE/ACM Trans Comput Biol Bioinform 3:334-46. 2006
    ..We also describe a linear-time algorithm to identify if two area cladograms are identical...
  16. pmc Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
    Md Shamsuzzoha Bayzid
    Department of Computer Science, University of Texas at Austin, Austin, Texas, USA
    PLoS ONE 10:e0129183. 2015
    ..New data used in this study are available at DOI: http://dx.doi.org/10.6084/m9.figshare.1411146, and the software is available at https://github.com/smirarab/binning. ..
  17. ncbi Reconstructing reticulate evolution in species-theory and practice
    Luay Nakhleh
    Department of Computer Science, Rice University, 6100 Main Street, MS 132, Houston, TX 77005, USA
    J Comput Biol 12:796-811. 2005
    ..Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison's method...
  18. pmc Fast and accurate methods for phylogenomic analyses
    Jimmy Yang
    Department of Computer Science, University of Texas at Austin, Austin TX 78712, USA
    BMC Bioinformatics 12:S4. 2011
    ..Relatively little is known about the relative performance of these methods...
  19. pmc PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
    Siavash Mirarab
    1 Department of Computer Science, University of Texas at Austin, Austin, Texas
    J Comput Biol 22:377-86. 2015
    ..Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory...
  20. pmc ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
    Siavash Mirarab
    Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA and Departments of Computer Science and Bioengineering, The University of Illinois at Urbana Champaign, Champaign, IL 61801, USA
    Bioinformatics 31:i44-52. 2015
    ..ASTRAL runs in polynomial time, by constraining the search space using a set of allowed 'bipartitions'. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent...
  21. doi Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree"
    Siavash Mirarab
    Department of Computer Science, University of Texas at Austin, Austin, TX, USA Department of Electrical and Computer Engineering, University of California at San Diego, San Diego, CA, USA
    Science 350:171. 2015
    ..Furthermore, their simulation study does not follow the recommended statistical binning protocol and has data of unknown origin that bias the results against weighted statistical binning. ..
  22. pmc An experimental study of Quartets MaxCut and other supertree methods
    M Shel Swenson
    Department of Computer Science, The University of Texas at Austin, Austin TX, USA
    Algorithms Mol Biol 6:7. 2011
    ..abstract:..