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‎.DS_Store‎

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‎PhyNEST_hc.log‎

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PhyNEST: Phylogenetic Network Estimation using SiTe patterns
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Analysis start: 2024-06-02 at 20:03:17
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Input file: example/sample_n5h1.txt
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Number of sequences: 5
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Sequence length: 1000000
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Starting Topology: (5,(2,(3,(4,1))));
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Outgroup specified for rooting: 5
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Number of maximum reticulation(s): 1
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The maximum number of iterations for each optimization: 1000
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Search algorithm selected: Hill climbing
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The maximum number of steps during search: 250000
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The maximum number of consecutive failures: 150 (using maximum_number_of_failures provided)
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Output file store directory: /Users/khaosan/Dropbox/PhyNESTp.jl
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The number of processors for this analysis: 1
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(1/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:17
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Starting topology changed to (5,(2,((4,3),1))); using nearest-neighbor interchange (NNI)
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The search terminated at step 80 and at 75th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 25 proposed, 0 accepted.
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Head move of reticulation edge: 25 proposed, 0 accepted.
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Change the direction of reticulation edge: 5 proposed, 1 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 23 proposed, 1 accepted.
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On the current topology, 96 moves were made, including 21 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(1/10) Estimated topology in this run: (5:3.771,(2:1.117,((1:0.933,(3:0.554,#H6:0.0::1.0):0.38):0.184,(4:0.554)#H6:0.563::0.0):0.0):2.654);
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(1/10) Composite likelihood of the estimated topology in this run: 4.830966179213048e6
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(2/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
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Starting topology changed to (5,((4,3),(2,1))); using nearest-neighbor interchange (NNI)
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The search terminated at step 102 and at 101th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 79 proposed, 0 accepted.
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Tail move of reticulation edge: 0 proposed, 0 accepted.
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Head move of reticulation edge: 0 proposed, 0 accepted.
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Change the direction of reticulation edge: 0 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 22 proposed, 0 accepted.
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On the current topology, 110 moves were made, including 9 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(2/10) Estimated topology in this run: (5:4.071,((4:1.336,3:1.336):0.0,(2:0.638,1:0.638):0.698):2.736);
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(2/10) Composite likelihood of the estimated topology in this run: 4.808939250517486e6
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(3/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
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Starting topology changed to (5,(1,((4,3),2))); using nearest-neighbor interchange (NNI)
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The search terminated at step 105 and at 104th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 81 proposed, 0 accepted.
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Tail move of reticulation edge: 0 proposed, 0 accepted.
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Head move of reticulation edge: 0 proposed, 0 accepted.
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Change the direction of reticulation edge: 0 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 23 proposed, 0 accepted.
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On the current topology, 110 moves were made, including 6 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(3/10) Estimated topology in this run: (5:3.865,(1:1.125,((4:1.125,3:1.125):0.0,2:1.125):0.0):2.739);
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(3/10) Composite likelihood of the estimated topology in this run: 4.832807714960081e6
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(4/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
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Starting topology changed to (5,(1,((4,2),3))); using nearest-neighbor interchange (NNI)
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The search terminated at step 92 and at 85th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 27 proposed, 1 accepted.
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Head move of reticulation edge: 25 proposed, 0 accepted.
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Change the direction of reticulation edge: 5 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 33 proposed, 0 accepted.
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On the current topology, 96 moves were made, including 11 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(4/10) Estimated topology in this run: (5:4.274,(#H6:0.807::0.0,(((2:0.709,(4:0.709)#H6:0.0::1.0):0.01,3:0.719):0.273,1:0.992):0.523):2.758);
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(4/10) Composite likelihood of the estimated topology in this run: 4.817041590497299e6
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(5/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:18
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Starting topology changed to (5,(1,(2,(3,4)))); using nearest-neighbor interchange (NNI)
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The search terminated at step 106 and at 75th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 29 proposed, 1 accepted.
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Head move of reticulation edge: 32 proposed, 0 accepted.
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Change the direction of reticulation edge: 10 proposed, 2 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 33 proposed, 1 accepted.
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On the current topology, 96 moves were made, including 21 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(5/10) Estimated topology in this run: (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
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(5/10) Composite likelihood of the estimated topology in this run: 4.741352247347821e6
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(6/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:20
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Starting topology changed to (5,(1,(4,(2,3)))); using nearest-neighbor interchange (NNI)
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The search terminated at step 81 and at 75th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 27 proposed, 1 accepted.
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Head move of reticulation edge: 25 proposed, 0 accepted.
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Change the direction of reticulation edge: 6 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 21 proposed, 0 accepted.
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On the current topology, 96 moves were made, including 21 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(6/10) Estimated topology in this run: (5:4.099,(#H6:0.57::0.0,(((2:0.632,3:0.632):0.314,(4:0.946)#H6:0.0::1.0):0.002,1:0.948):0.567):2.584);
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(6/10) Composite likelihood of the estimated topology in this run: 4.79908686476507e6
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(7/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:20
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Starting topology remains unchanged
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The search terminated at step 131 and at 75th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 38 proposed, 1 accepted.
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Head move of reticulation edge: 42 proposed, 2 accepted.
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Change the direction of reticulation edge: 13 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 36 proposed, 1 accepted.
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On the current topology, 96 moves were made, including 21 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(7/10) Estimated topology in this run: (5:10.28,(((1:2.363,(2:0.376,(3:0.376)#H6:0.0::0.379):1.988):1.268,#H6:3.255::0.621):1.572,4:5.202):5.077);
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(7/10) Composite likelihood of the estimated topology in this run: 4.741362031645942e6
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(8/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:32
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Starting topology changed to (5,((2,3),(1,4))); using nearest-neighbor interchange (NNI)
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The search terminated at step 108 and at 107th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 83 proposed, 0 accepted.
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Tail move of reticulation edge: 0 proposed, 0 accepted.
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Head move of reticulation edge: 0 proposed, 0 accepted.
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Change the direction of reticulation edge: 0 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 24 proposed, 0 accepted.
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On the current topology, 111 moves were made, including 4 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(8/10) Estimated topology in this run: (5:4.076,((2:0.638,3:0.638):0.7,(1:1.338,4:1.338):0.0):2.738);
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(8/10) Composite likelihood of the estimated topology in this run: 4.808848819713962e6
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(9/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:32
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Starting topology changed to (5,((3,(1,4)),2)); using nearest-neighbor interchange (NNI)
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The search terminated at step 140 and at 86th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 2 proposed, 1 accepted.
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Tail move of reticulation edge: 45 proposed, 4 accepted.
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Head move of reticulation edge: 34 proposed, 0 accepted.
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Change the direction of reticulation edge: 11 proposed, 2 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 47 proposed, 0 accepted.
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On the current topology, 96 moves were made, including 10 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(9/10) Estimated topology in this run: (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);
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(9/10) Composite likelihood of the estimated topology in this run: 4.741344634057323e6
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(10/10) Searching for the best network using the hill climbing algorithm; 2024-06-02 at 20:03:39
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Starting topology changed to (5,(3,(2,(1,4)))); using nearest-neighbor interchange (NNI)
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The search terminated at step 79 and at 75th consecutive failures.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 26 proposed, 1 accepted.
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Head move of reticulation edge: 25 proposed, 0 accepted.
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Change the direction of reticulation edge: 5 proposed, 0 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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NNI: 21 proposed, 0 accepted.
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On the current topology, 96 moves were made, including 21 unsuccessful moves.
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Terminated although it neither reached the maximum number of steps or failures,
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possibly because there was no more move to make.
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(10/10) Estimated topology in this run: (5:3.743,(#H6:0.425::0.847,((2:0.96,((1:1.385,4:1.385):0.0)#H6:0.0::0.153):0.0,3:0.96):0.425):2.358);
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(10/10) Composite likelihood of the estimated topology in this run: 4.822329367341726e6
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Summary:
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Run Composite likelihood Network estimated
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1 4.8309662e6 (5:3.771,(2:1.117,((1:0.933,(3:0.554,#H6:0.0::1.0):0.38):0.184,(4:0.554)#H6:0.563::0.0):0.0):2.654);
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2 4.8089393e6 (5:4.071,((4:1.336,3:1.336):0.0,(2:0.638,1:0.638):0.698):2.736);
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3 4.8328077e6 (5:3.865,(1:1.125,((4:1.125,3:1.125):0.0,2:1.125):0.0):2.739);
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4 4.8170416e6 (5:4.274,(#H6:0.807::0.0,(((2:0.709,(4:0.709)#H6:0.0::1.0):0.01,3:0.719):0.273,1:0.992):0.523):2.758);
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5 4.7413522e6 (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
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6 4.7990869e6 (5:4.099,(#H6:0.57::0.0,(((2:0.632,3:0.632):0.314,(4:0.946)#H6:0.0::1.0):0.002,1:0.948):0.567):2.584);
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7 4.741362e6 (5:10.28,(((1:2.363,(2:0.376,(3:0.376)#H6:0.0::0.379):1.988):1.268,#H6:3.255::0.621):1.572,4:5.202):5.077);
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8 4.8088488e6 (5:4.076,((2:0.638,3:0.638):0.7,(1:1.338,4:1.338):0.0):2.738);
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9 4.7413446e6 (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);
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10 4.8223294e6 (5:3.743,(#H6:0.425::0.847,((2:0.96,((1:1.385,4:1.385):0.0)#H6:0.0::0.153):0.0,3:0.96):0.425):2.358);
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Best topology: (5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);)
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End;

‎PhyNEST_hc.out‎

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(5:9.873,(((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981,4:4.979):4.894);
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(5:9.873,(((3:1.57,(2:1.43)#H6:0.14):1.427,(#H6:0.0,1:1.43):1.567):1.981,4:4.979):4.894);

‎PhyNEST_sa.log‎

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PhyNEST: Phylogenetic Network Estimation using SiTe patterns
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Analysis start: 2024-06-02 at 20:03:58
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Input file: example/sample_n5h1.txt
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Number of sequences: 5
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Sequence length: 1000000
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Starting Topology: (5,(2,(3,(4,1))));
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Outgroup specified for rooting: 5
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Number of maximum reticulation(s): 1
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The maximum number of iterations for each optimization: 1000
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Search algorithm selected: Simulated annealing with alpha=0.5; c=0.5
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The maximum number of steps during search: 250000
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The maximum number of consecutive failures: 50 (computed using probN=9.5e-45 provided.)
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Output file store directory: /Users/khaosan/Dropbox/PhyNESTp.jl
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The number of processors for this analysis: 1
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(1/2) Searching for the best network using the simulated annealing algorithm; 2024-06-02 at 20:03:59
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Starting topology remains unchanged
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Running 25 burn-ins...
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Burn in complete. At most -log likelihood value can change 253831.89630290028 at a single step.
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Showing 10 best topologies found in this run:
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Rank Composite Likelihood Network
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1 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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2 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981):4.894);
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3 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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4 4.74135224735e6 (5:10.27,(4:5.197,((3:2.358,(2:0.38,#H6:0.0::0.62):1.978):1.273,(1:0.38)#H6:3.25::0.38):1.566):5.073);
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The total length of best trees is shorter than k.
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Speciation times for some newicks may not have updated if estimates are weird (e.g., NaN).
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The search terminated at step 585 and at 50th consecutive failures and (Cooling schedule)ci=2154.7764941621217.
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Summary of each move:
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Insertion of reticulation edge: 2 proposed, 1 accepted.
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Tail move of reticulation edge: 165 proposed, 106 accepted.
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Head move of reticulation edge: 133 proposed, 44 accepted.
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Change the direction of reticulation edge: 122 proposed, 37 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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Nearest-neighbor interchange (NNI): 163 proposed, 9 accepted.
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On the current topology, 68 moves were made, including 18 unsuccessful moves.
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Terminated because it reached the maximum number of failures (current maximum_number_of_failures=50).
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(1/2) Estimated topology in this run: (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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(1/2) Composite likelihood of the estimated topology in this run: 4.741344634057322e6
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(2/2) Searching for the best network using the simulated annealing algorithm; 2024-06-02 at 20:05:13
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Starting topology remains unchanged
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Running 25 burn-ins...
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Burn in complete. At most -log likelihood value can change 276213.0673120329 at a single step.
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Showing 10 best topologies found in this run:
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Rank Composite Likelihood Network
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1 4.74134463406e6 (5:9.873,(4:4.979,((1:1.43,(2:1.43)#H6:0.0::0.475):1.567,(3:1.57,#H6:0.14::0.525):1.427):1.981):4.894);
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2 4.74134463406e6 (5:9.873,(((1:1.43,(2:1.43)#H6:0.0::0.475):1.567,(#H6:0.14::0.525,3:1.57):1.427):1.981,4:4.979):4.894);
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3 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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4 4.74134463406e6 (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.525):1.567,((2:1.43)#H6:0.14::0.475,3:1.57):1.427):1.981):4.894);
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5 4.74134463406e6 (5:9.873,(4:4.979,((#H6:0.0::0.525,1:1.43):1.567,((2:1.43)#H6:0.14::0.475,3:1.57):1.427):1.981):4.894);
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6 4.74134463406e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(#H6:0.0::0.475,1:1.43):1.567):1.981):4.894);
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The total length of best trees is shorter than k.
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Speciation times for some newicks may not have updated if estimates are weird (e.g., NaN).
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The search terminated at step 910 and at 50th consecutive failures and (Cooling schedule)ci=1512.6720311686329.
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Summary of each move:
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Insertion of reticulation edge: 1 proposed, 1 accepted.
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Tail move of reticulation edge: 251 proposed, 131 accepted.
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Head move of reticulation edge: 228 proposed, 69 accepted.
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Change the direction of reticulation edge: 216 proposed, 95 accepted.
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Deletion of reticulation edge: 0 proposed, 0 accepted.
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Nearest-neighbor interchange (NNI): 214 proposed, 14 accepted.
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On the current topology, 66 moves were made, including 16 unsuccessful moves.
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Terminated because it reached the maximum number of failures (current maximum_number_of_failures=50).
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(2/2) Estimated topology in this run: (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.475):1.567,(3:1.57,(2:1.43)#H6:0.14::0.525):1.427):1.981):4.894);
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(2/2) Composite likelihood of the estimated topology in this run: 4.741344634057322e6
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Summary:
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Run Composite likelihood Network estimated
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1 4.7413446e6 (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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2 4.7413446e6 (5:9.873,(4:4.979,((1:1.43,#H6:0.0::0.475):1.567,(3:1.57,(2:1.43)#H6:0.14::0.525):1.427):1.981):4.894);
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Best topology: (5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);)
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End;

‎PhyNEST_sa.out‎

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(5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14::0.525):1.427,(1:1.43,#H6:0.0::0.475):1.567):1.981):4.894);
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(5:9.873,(4:4.979,((3:1.57,(2:1.43)#H6:0.14):1.427,(1:1.43,#H6:0.0):1.567):1.981):4.894);

‎Project.toml‎

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name = "PhyNEST"
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uuid = "115de871-c282-4823-a74f-b03678acf966"
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authors = ["Sungsik Kong"]
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version = "0.1.11"
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version = "0.1.12"
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[deps]
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

‎docs/src/index.md‎

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PhyNEST.GetTrueProbsAsymmTypes
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PhyNEST.sim_sp_freq
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PhyNEST.phyne!
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PhyNEST.Dstat

‎example/.DS_Store‎

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