Advances in phylogeny reconstruction from gene order and content data.

[1]  Jijun Tang,et al.  Reconstructing phylogenies from gene-content and gene-order data , 2007, Mathematics of Evolution and Phylogeny.

[2]  Tzvika Hartman,et al.  A 1.375-Approximation Algorithm for Sorting by Transpositions , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[3]  Tandy J. Warnow,et al.  Distance-Based Genome Rearrangement Phylogeny , 2006, Journal of Molecular Evolution.

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[8]  Bernard M. E. Moret,et al.  Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data , 2004, WABI.

[9]  Roded Sharan,et al.  A 1.5-approximation algorithm for sorting by transpositions and transreversals , 2004, J. Comput. Syst. Sci..

[10]  Bernard M. E. Moret,et al.  Rec-I-DCM3: a fast algorithmic technique for reconstructing phylogenetic trees , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[11]  Binhai Zhu,et al.  A Linear-Time Algorithm for Computing Translocation Distance between Signed Genomes , 2004, CPM.

[12]  Marie-France Sagot,et al.  Sorting by Reversals in Subquadratic Time , 2004, CPM.

[13]  Jijun Tang,et al.  Phylogenetic reconstruction from arbitrary gene-order data , 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

[14]  Steven Skiena,et al.  Improved bounds on sorting with length-weighted reversals , 2004, SODA '04.

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[17]  Tandy J. Warnow,et al.  Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees , 2004, IEEE Computer Society Computational Systems Bioinformatics Conference.

[18]  Jijun Tang,et al.  Large-scale phylogenetic reconstruction from arbitrary gene-order data , 2004 .

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[20]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[21]  Jijun Tang,et al.  Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content , 2003, WADS.

[22]  Krister M. Swenson,et al.  Genomic Distances under Deletions and Insertions , 2003, COCOON.

[23]  David Sankoff,et al.  Detection and validation of single gene inversions , 2003, ISMB.

[24]  Jijun Tang,et al.  Scaling up accurate phylogenetic reconstruction from gene-order data , 2003, ISMB.

[25]  Tzvika Hartman,et al.  A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions , 2003, CPM.

[26]  P. Pevzner,et al.  Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

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[28]  T. Warnow,et al.  Large-scale phylogenetic analysis , 2003 .

[29]  Tandy J. Warnow,et al.  Steps toward accurate reconstructions of phylogenies from gene-order data , 2002, J. Comput. Syst. Sci..

[30]  Glenn Tesler,et al.  Efficient algorithms for multichromosomal genome rearrangements , 2002, J. Comput. Syst. Sci..

[31]  J. Kadane,et al.  Bayesian phylogenetic inference from animal mitochondrial genome arrangements , 2002 .

[32]  Tao Liu,et al.  Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data , 2002, WABI.

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

[34]  Tandy J. Warnow,et al.  Toward new software for computational phylogenetics , 2002, Computer.

[35]  Tandy J. Warnow,et al.  The Accuracy of Fast Phylogenetic Methods for Large Datasets , 2001, Pacific Symposium on Biocomputing.

[36]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[37]  Bernard M. E. Moret,et al.  New Software for Computational Phylogenetics , 2002 .

[38]  Bernard M. E. Moret,et al.  Fast Phylogenetic Methods For Genome Rearrangement Evolution: An Empirical Study , 2002 .

[39]  P. Pevzner,et al.  Genome-scale evolution: reconstructing gene orders in the ancestral species. , 2002, Genome research.

[40]  Sudhir Kumar,et al.  MEGA2: molecular evolutionary genetics analysis software , 2001, Bioinform..

[41]  Bernard M. E. Moret,et al.  Finding an Optimal Inversion Median: Experimental Results , 2001, WABI.

[42]  Tandy J. Warnow,et al.  The Performance of Phylogenetic Methods on Trees of Bounded Diameter , 2001, WABI.

[43]  Alberto Caprara,et al.  On the Practical Solution of the Reversal Median Problem , 2001, WABI.

[44]  David A. Bader,et al.  A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study , 2001, WADS.

[45]  Tandy J. Warnow,et al.  Estimating true evolutionary distances between genomes , 2001, STOC '01.

[46]  Tandy J. Warnow,et al.  New approaches for reconstructing phylogenies from gene order data , 2001, ISMB.

[47]  Tandy J. Warnow,et al.  Designing fast converging phylogenetic methods , 2001, ISMB.

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[52]  Tandy J. Warnow,et al.  A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data , 2000, ISMB.

[53]  Nadia El-Mabrouk,et al.  Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments , 2000, CPM.

[54]  Bin Ma,et al.  From Gene Trees to Species Trees , 2000, SIAM J. Comput..

[55]  Brendan D. McKay,et al.  TrExML: a maximum-likelihood approach for extensive tree-space exploration , 2000, Bioinform..

[56]  A. Halpern,et al.  Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. , 2000, Molecular biology and evolution.

[57]  Maria Emilia M. T. Walter,et al.  Reversal Distance of Signed Circular Chromosomes , 2000 .

[58]  Bernard M. E. Moret,et al.  An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae , 2000 .

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[62]  David Sankoff,et al.  Genome rearrangement with gene families , 1999, Bioinform..

[63]  Daniel H. Huson,et al.  Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction , 1999, J. Comput. Biol..

[64]  Kevin Atteson,et al.  The Performance of Neighbor-Joining Methods of Phylogenetic Reconstruction , 1999, Algorithmica.

[65]  Alberto Caprara,et al.  Formulations and hardness of multiple sorting by reversals , 1999, RECOMB.

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[67]  J. Boore,et al.  Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. , 1998, Current opinion in genetics & development.

[68]  Bin Ma,et al.  On reconstructing species trees from gene trees in term of duplications and losses , 1998, RECOMB '98.

[69]  David Sankoff,et al.  Multiple Genome Rearrangement and Breakpoint Phylogeny , 1998, J. Comput. Biol..

[70]  Ron Shamir,et al.  The median problems for breakpoints are NP-complete , 1998, Electron. Colloquium Comput. Complex..

[71]  Roderic D. M. Page,et al.  GeneTree: comparing gene and species phylogenies using reconciled trees , 1998, Bioinform..

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[73]  O Gascuel,et al.  BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.

[74]  R. Page,et al.  From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. , 1997, Molecular phylogenetics and evolution.

[75]  Arne Ø. Mooers,et al.  Inferring Evolutionary Process from Phylogenetic Tree Shape , 1997, The Quarterly Review of Biology.

[76]  David Sankoff,et al.  Conserved segment identification , 1997, RECOMB '97.

[77]  Haim Kaplan,et al.  Faster and simpler algorithm for sorting signed permutations by reversals , 1997, SODA '97.

[78]  David Sankoff,et al.  Conserved Synteny As a Measure of Genomic Distance , 1996, Discret. Appl. Math..

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