computing the quartet distance between general trees

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74 APPENDIX C. REAL-LIFE APPLICATION OF THE ALGORITHMHowever, I later provided my C++ implementation that does the job in a few seconds andafter wrapping it as a module for Python it worked painlessly with their software:The new algorithm is exactly what we needed, and it will be quite useful.Foster provided an example of a master tree and a QJ tree made from some subsetsof the master tree. They are displayed in Fig. C.1 and we can observe that they do indeedinclude polytomies. The quartet distance between the two trees is 317524.
75t29t25t54t20t27 t13 t1t3t17t24t41t49t7t14t28t53t15t36t10t47t6t0t43t57t48t45t9t31t30t59t56t42t51t4t39t5t2t8t18t33t19t11t38t35t23t52t40t50t37t34t55t46t21t16t58t22t26t44t12t32t11t4t39t8t18 t33 t35t50t52t34t46t38t55t5t6t30t47t51t15t42t7t2t9t13t31t3t43t1t10t0t12t56t14t53t16t49t21t59t48t58t22t57t26t45t44t41t32t37t17t36t28t24t40t23t29t25t54t27t20t19Figure C.1: An example of a master tree and a reconstruction of the master tree by quartet joining.
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Master’s thesisCOMPUTING THE QUAR
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AcknowledgementsFirst of all I woul
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viiiCONTENTS5.3 Implementing leaf s
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2 CHAPTER 1. INTRODUCTIONhas is cal
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4 CHAPTER 1. INTRODUCTIONIt is evid
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6 CHAPTER 1. INTRODUCTIONsub-cubic
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Chapter 2PrerequisitesFirst, this c
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2.2. CHOICE OF LANGUAGE AND TEST EN
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14 CHAPTER 3. EXPERIMENTAL APPROACH
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20 CHAPTER 4. QUARTIC TIME ALGORITH
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22 CHAPTER 4. QUARTIC TIME ALGORITH
Page 33 and 34: Chapter 5Calculating leaf set sizes
Page 35 and 36: 5.3. IMPLEMENTING LEAF SET ALGORITH
Page 37 and 38: 5.3. IMPLEMENTING LEAF SET ALGORITH
Page 39 and 40: Chapter 6Cubic time algorithmHere I
Page 41 and 42: 6.1. IMPLEMENTATION 33that we can l
Page 43 and 44: 6.1. IMPLEMENTATION 35carried out o
Page 45 and 46: Chapter 7Sub-cubic time algorithmIn
Page 47 and 48: 7.1. THE ALGORITHM 39CcabADFigure 7
Page 49 and 50: 7.1. THE ALGORITHM 41reflecting Eq.
Page 51 and 52: 7.1. THE ALGORITHM 43choice of indi
Page 53 and 54: 7.1. THE ALGORITHM 45More interesti
Page 55 and 56: 7.2. IMPLEMENTATION 477.2 Implement
Page 57 and 58: 7.2. IMPLEMENTATION 49tween the num
Page 59 and 60: 7.2. IMPLEMENTATION 51oretic approa
Page 61 and 62: 7.2. IMPLEMENTATION 53well. My impl
Page 63 and 64: 7.2. IMPLEMENTATION 55Performance o
Page 65: 7.2. IMPLEMENTATION 57ble sort, wil
Page 68 and 69: 60 CHAPTER 8. RESULTS AND DISCUSSIO
Page 71 and 72: Chapter 9ConclusionThe focus of thi
Page 73 and 74: Bibliography[1] Mukul S. Bansal, Ji
Page 75: BIBLIOGRAPHY 67[20] M.S. Waterman a
Page 78 and 79: 70 APPENDIX A. PREPROCESSING FOR TH
Page 81: Appendix CReal-life application of
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