MRL and SuperFine+MRL: new supertree methods

[1]  João Luís Sobral,et al.  Parallelizing SuperFine , 2012, SAC '12.

[2]  Tandy Warnow,et al.  SuperFine: fast and accurate supertree estimation. , 2012, Systematic biology.

[3]  Mike Steel,et al.  Terraces in Phylogenetic Tree Space , 2011, Science.

[4]  Arndt von Haeseler,et al.  Accuracy of phylogeny reconstruction methods combining overlapping gene data sets , 2010, Algorithms for Molecular Biology.

[5]  Tandy J. Warnow,et al.  An experimental study of Quartets MaxCut and other supertree methods , 2010, Algorithms for Molecular Biology.

[6]  Vincent Ranwez,et al.  SuperTriplets: a triplet-based supertree approach to phylogenomics , 2010, Bioinform..

[7]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[8]  David Fernández-Baca,et al.  Robinson-Foulds Supertrees , 2010, Algorithms for Molecular Biology.

[9]  Tandy J. Warnow,et al.  A simulation study comparing supertree and combined analysis methods using SMIDGen , 2009, Algorithms for Molecular Biology.

[10]  Serita M. Nelesen,et al.  Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees , 2009, Science.

[11]  Michelle Dawn Swenson,et al.  Phylogenetic supertree methods , 2009 .

[12]  Pablo A. Goloboff,et al.  TNT, a free program for phylogenetic analysis , 2008 .

[13]  Sylvain Guillemot,et al.  PhySIC: a veto supertree method with desirable properties. , 2007, Systematic biology.

[14]  Mike Steel,et al.  Maximum likelihood supertrees. , 2007, Systematic biology.

[15]  Pablo A Goloboff,et al.  On divide-and-conquer strategies for parsimony analysis of large data sets: Rec-I-DCM3 versus TNT. , 2007, Systematic biology.

[16]  Mark Wilkinson,et al.  Majority-rule supertrees. , 2007, Systematic biology.

[17]  Andy Purvis,et al.  A higher-level MRP supertree of placental mammals , 2006, BMC Evolutionary Biology.

[18]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[19]  M. Sanderson,et al.  Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. , 2006, Systematic biology.

[20]  David Fernández-Baca,et al.  Minimum-flip supertrees: complexity and algorithms , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[21]  Sébastien Roch,et al.  A short proof that phylogenetic tree reconstruction by maximum likelihood is hard , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[22]  Thomas Ludwig,et al.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees , 2005, Bioinform..

[23]  O. Bininda-Emonds.  Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life , 2004 .

[24]  Andy Purvis,et al.  A species-level phylogenetic supertree of marsupials , 2004 .

[25]  Tandy J. Warnow,et al.  On contract-and-refine transformations between phylogenetic trees , 2004, SODA '04.

[26]  Tandy J. Warnow,et al.  Sequence-Length Requirements for Phylogenetic Methods , 2002, WABI.

[27]  M Steel,et al.  Links between maximum likelihood and maximum parsimony under a simple model of site substitution. , 1997, Bulletin of mathematical biology.

[28]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[29]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[30]  R. Graham,et al.  The steiner problem in phylogeny is NP-complete , 1982 .

[31]  Serita M. Nelesen,et al.  SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. , 2012, Systematic biology.

[32]  Satish Rao,et al.  Quartet MaxCut: a fast algorithm for amalgamating quartet trees. , 2012, Molecular phylogenetics and evolution.

[33]  Tandy Warnow,et al.  Multiple sequence alignment: a major challenge to large-scale phylogenetics. , 2010, PLoS currents.

[34]  Carito Guziolowski,et al.  Algorithms for Molecular Biology , 2007 .

[35]  Mark A. Ragan,et al.  The MRP Method , 2004 .

[36]  David Fernández-Baca,et al.  Mrf Supertrees , 2004 .

[37]  M. Kennedy,et al.  SEABIRD SUPERTREES: COMBINING PARTIAL ESTIMATES OF PROCELLARIIFORM PHYLOGENY , 2002 .

[38]  Michael J. Sanderson,et al.  MOLECULAR PHYLOGENY OF THE "TEMPERATE HERBACEOUS TRIBES" OF PAPILIONOID LEGUMES: A SUPERTREE APPROACH , 2000 .

[39]  Tao Jiang,et al.  On the Complexity of Multiple Sequence Alignment , 1994, J. Comput. Biol..

[40]  D. Ord,et al.  PAUP:Phylogenetic analysis using parsi-mony , 1993 .