Refined Buneman Trees

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Refined Buneman Trees Lasse Westh-N
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This thesis is dedicated to my fami
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Contents 1 Introduction 7 1.1 Docum
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13.3 Correctness of the reference i
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The theory of evolution has also be
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Chapter 2 Definitions This chapter
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A C B Figure 2.1: An evolutionary t
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2.4 Quartets To every set of four s
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2.6 Splits The partition of a finit
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evolutionary tree gives an invaluab
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time in the algorithm. In [BFÖ+ 03
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Figure 3.1: A tree of life. 22
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knowing its origins, but how does h
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anging from huge time complexity to
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Algorithm 2 The Neighbor-Joining al
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A, C, T 1 2 3 T A, C, T T C, T A, T
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Part II Implementing Refined Bunema
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Algorithm 3 Overapproximating the r
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the pseudo-code for the algorithm i
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AE DE D B e E BC A C BE AC Figure 5
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construction, but we still have to
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Chapter 6 TheTreeDataStructure This
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incidentedge Figure 6.2: The world
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interface EdgeIterator { boolean ha
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Figure 6.7: An example a node which
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So how do we find σ ′ We start
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Algorithm 5. Offhand, the algorithm
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Algorithm 6 The algorithm that calc
Page 57 and 58: a b c d root ab cd Figure 8.2: Upda
Page 59 and 60: 6000 Quad Tree performance characte
Page 61 and 62: 30000 Quad Tree performance charact
Page 63 and 64: sets A, B, C and D by scanning the
Page 65 and 66: Chapter 10 The Selection Algorithm
Page 67 and 68: is O(n 2 ). The algorithm uses a di
Page 69 and 70: Chapter 11 JSplits Figure 11.1: A s
Page 71 and 72: implementing an algorithm with a hi
Page 73 and 74: Chapter 12 Source Code The source c
Page 75 and 76: Chapter 13 The Reference Implementa
Page 77 and 78: • the splits that are generated.
Page 79 and 80: Chapter 14 Correctness This chapter
Page 81 and 82: The best possible way of testing wo
Page 83 and 84: 100000 90000 Performance of the ref
Page 85 and 86: of the size of the heap during the
Page 87 and 88: 140000 Space complexity best fit: x
Page 89 and 90: Chapter 16 Comparing Evolutionary T
Page 91 and 92: Figure 16.1: The size of the set B(
Page 93 and 94: Figure 16.2: The total number of sp
Page 95 and 96: that it over-induces splits, and th
Page 97 and 98: efined Buneman therefore suffers a
Page 99 and 100: Speedups might be achieved using op
Page 101 and 102: Appendix A Correctness of the Refer
Page 103 and 104: Quartet: 0 0 | 1 4 -0.1263501163396
Page 105 and 106: Appendix B Garbage Collector Log 0.
Page 107: Bibliography [AJL + 02] Bruce Alber
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