Exact Algorithms for the Reversal Median Problem

OF THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science Computer Science The University of New Mexico Albuquerque, New Mexico

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

[2]  Walter M. Fitch,et al.  On the Problem of Discovering the Most Parsimonious Tree , 1977, The American Naturalist.

[3]  Kenneth H. Wolfe,et al.  High Frequency of Inversions During Eukaryote Gene Order Evolution , 2000 .

[4]  Anne Bergeron,et al.  A very elementary presentation of the Hannenhalli-Pevzner theory , 2005, Discret. Appl. Math..

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

[6]  D. Sankoff,et al.  Parametric genome rearrangement. , 1996, Gene.

[7]  Jo Dicks.  Chromtree: Maximum Likelihood Estimation of Chromosomal Phylogenies , 2000 .

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

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

[10]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[11]  T. Dobzhansky,et al.  Inversions in the Chromosomes of Drosophila Pseudoobscura. , 1938, Genetics.

[12]  Pavel A. Pevzner,et al.  Computational molecular biology : an algorithmic approach , 2000 .

[13]  Jon Kleinberg,et al.  Algorithms for Constructing Comparative Maps , 2000 .

[14]  Pavel A. Pevzner,et al.  Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals , 1995, JACM.

[15]  Anne Bergeron,et al.  Experiments in Computing Sequences of Reversals , 2001, WABI.

[16]  D. Sankoff,et al.  Duplication, Rearrangement, and Reconciliation , 2000 .

[17]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

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

[19]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

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

[21]  Alberto Caprara,et al.  Sorting by reversals is difficult , 1997, RECOMB '97.

[22]  David Sankoff,et al.  Early eukaryote evolution based on mitochondrial gene order breakpoints , 2000, RECOMB '00.

[23]  Piotr Berman,et al.  Fast Sorting by Reversal , 1996, CPM.

[24]  Pavel A. Pevzner,et al.  Transforming men into mice (polynomial algorithm for genomic distance problem) , 1995, Proceedings of IEEE 36th Annual Foundations of Computer Science.

[25]  Christos H. Papadimitriou,et al.  Bounds for sorting by prefix reversal , 1979, Discret. Math..

[26]  D. Sankoff,et al.  Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Joseph Felsenstein,et al.  Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters , 1973 .

[28]  João Meidanis,et al.  Introduction to computational molecular biology , 1997 .

[29]  W. Ewens,et al.  The chromosome inversion problem , 1982 .

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

[31]  L. Cavalli-Sforza,et al.  PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES , 1967, Evolution; international journal of organic evolution.

[32]  P A Pevzner,et al.  Genome sequence comparison and scenarios for gene rearrangements: a test case. , 1995, Genomics.

[33]  David Waddington,et al.  Estimating the Number of Conserved Segments Between Species Using a Chromosome Based Model , 2000 .