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Update explanations
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BenjaminDoran committed Feb 6, 2024
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4 changes: 1 addition & 3 deletions README.md
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Expand Up @@ -18,10 +18,8 @@ To (locally) reproduce this project, do the following:

0. Download this code base.
```
git clone [email protected]:aramanlab/Doran_etal_2023.git
git clone --recurse-submodules [email protected]:aramanlab/Doran_etal_2023.git
cd Doran_etal_2023
git submodule init
git submodule update
```
1. Open a Julia console and do:
```
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2 changes: 1 addition & 1 deletion data/exp_pro/BB669/BB669-tree.nw

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82 changes: 41 additions & 41 deletions data/exp_pro/localsweep/TableS1.csv
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@@ -1,50 +1,50 @@
msaname,ntaxa,nfeatures,chartype,SPI_fscore,SPI_recall,SPI_precision
balancedtree-t1024-s42-l1024-b2,1024,1024,DNA,0.7748583204533745,0.735812133072407,0.8182807399347116
balancedtree-t1024-s42-l128-b2,1024,128,DNA,0.7180548370408691,0.6790606653620352,0.7618002195389681
balancedtree-t1024-s42-l16-b2,1024,16,DNA,0.026565464895635674,0.0136986301369863,0.4375
balancedtree-t1024-s42-l256-b2,1024,256,DNA,0.7201646090534979,0.684931506849315,0.7592190889370932
balancedtree-t1024-s42-l32-b2,1024,32,DNA,0.36014760147601477,0.23874755381604695,0.7327327327327328
balancedtree-t1024-s42-l512-b2,1024,512,DNA,0.7535641547861507,0.7240704500978473,0.7855626326963907
balancedtree-t1024-s42-l64-b2,1024,64,DNA,0.6468682505399568,0.586105675146771,0.7216867469879518
balancedtree-t1024-s42-l1024-b2,1024,1024,DNA,0.7711468604047743,0.7270058708414873,0.8209944751381215
balancedtree-t1024-s42-l128-b2,1024,128,DNA,0.7157676348547718,0.675146771037182,0.7615894039735099
balancedtree-t1024-s42-l16-b2,1024,16,DNA,0.0303030303030303,0.015655577299412915,0.47058823529411764
balancedtree-t1024-s42-l256-b2,1024,256,DNA,0.7211093990755008,0.6868884540117417,0.7589189189189189
balancedtree-t1024-s42-l32-b2,1024,32,DNA,0.3476297968397291,0.22602739726027396,0.752442996742671
balancedtree-t1024-s42-l512-b2,1024,512,DNA,0.7512742099898064,0.7211350293542075,0.7840425531914894
balancedtree-t1024-s42-l64-b2,1024,64,DNA,0.640480087288598,0.5743639921722113,0.7237977805178791
balancedtree-t128-s42-l1024-b2,128,1024,DNA,0.8442622950819672,0.8174603174603174,0.8728813559322034
balancedtree-t128-s42-l128-b2,128,128,DNA,0.825,0.7857142857142857,0.868421052631579
balancedtree-t128-s42-l16-b2,128,16,DNA,0.05970149253731343,0.031746031746031744,0.5
balancedtree-t128-s42-l256-b2,128,256,DNA,0.759493670886076,0.7142857142857143,0.8108108108108109
balancedtree-t128-s42-l32-b2,128,32,DNA,0.36046511627906974,0.24603174603174602,0.6739130434782609
balancedtree-t128-s42-l512-b2,128,512,DNA,0.7736625514403291,0.746031746031746,0.8034188034188035
balancedtree-t128-s42-l64-b2,128,64,DNA,0.4734299516908213,0.3888888888888889,0.6049382716049383
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balancedtree-t16-s42-l128-b2,16,128,DNA,0.8571428571428571,0.8571428571428571,0.8571428571428571
balancedtree-t16-s42-l16-b2,16,16,DNA,0.21052631578947364,0.14285714285714285,0.4
balancedtree-t128-s42-l128-b2,128,128,DNA,0.8200836820083682,0.7777777777777778,0.8672566371681416
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balancedtree-t128-s42-l256-b2,128,256,DNA,0.7606837606837606,0.7063492063492064,0.8240740740740741
balancedtree-t128-s42-l32-b2,128,32,DNA,0.3720930232558139,0.25396825396825395,0.6956521739130435
balancedtree-t128-s42-l512-b2,128,512,DNA,0.7836734693877551,0.7619047619047619,0.8067226890756303
balancedtree-t128-s42-l64-b2,128,64,DNA,0.48309178743961345,0.3968253968253968,0.6172839506172839
balancedtree-t16-s42-l1024-b2,16,1024,DNA,0.7142857142857143,0.7142857142857143,0.7142857142857143
balancedtree-t16-s42-l128-b2,16,128,DNA,0.8148148148148148,0.7857142857142857,0.8461538461538461
balancedtree-t16-s42-l16-b2,16,16,DNA,0.3157894736842105,0.21428571428571427,0.6
balancedtree-t16-s42-l256-b2,16,256,DNA,0.7692307692307692,0.7142857142857143,0.8333333333333334
balancedtree-t16-s42-l32-b2,16,32,DNA,0.56,0.5,0.6363636363636364
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balancedtree-t16-s42-l512-b2,16,512,DNA,0.6153846153846153,0.5714285714285714,0.6666666666666666
balancedtree-t16-s42-l64-b2,16,64,DNA,0.7857142857142857,0.7857142857142857,0.7857142857142857
balancedtree-t256-s42-l1024-b2,256,1024,DNA,0.7714285714285715,0.7440944881889764,0.8008474576271186
balancedtree-t256-s42-l128-b2,256,128,DNA,0.7484407484407484,0.7086614173228346,0.7929515418502202
balancedtree-t256-s42-l16-b2,256,16,DNA,0.05797101449275362,0.031496062992125984,0.36363636363636365
balancedtree-t256-s42-l256-b2,256,256,DNA,0.7835051546391752,0.7480314960629921,0.8225108225108225
balancedtree-t256-s42-l32-b2,256,32,DNA,0.4239130434782609,0.30708661417322836,0.6842105263157895
balancedtree-t256-s42-l512-b2,256,512,DNA,0.7515400410677617,0.7204724409448819,0.7854077253218884
balancedtree-t256-s42-l64-b2,256,64,DNA,0.6233766233766234,0.5669291338582677,0.6923076923076923
balancedtree-t256-s42-l128-b2,256,128,DNA,0.755741127348643,0.7125984251968503,0.8044444444444444
balancedtree-t256-s42-l16-b2,256,16,DNA,0.07142857142857144,0.03937007874015748,0.38461538461538464
balancedtree-t256-s42-l256-b2,256,256,DNA,0.7791666666666667,0.7362204724409449,0.827433628318584
balancedtree-t256-s42-l32-b2,256,32,DNA,0.4324324324324325,0.31496062992125984,0.6896551724137931
balancedtree-t256-s42-l512-b2,256,512,DNA,0.7520325203252034,0.7283464566929134,0.7773109243697479
balancedtree-t256-s42-l64-b2,256,64,DNA,0.648068669527897,0.594488188976378,0.7122641509433962
balancedtree-t32-s42-l1024-b2,32,1024,DNA,0.896551724137931,0.8666666666666667,0.9285714285714286
balancedtree-t32-s42-l128-b2,32,128,DNA,0.8275862068965518,0.8,0.8571428571428571
balancedtree-t32-s42-l16-b2,32,16,DNA,0.16666666666666669,0.1,0.5
balancedtree-t32-s42-l256-b2,32,256,DNA,0.7017543859649122,0.6666666666666666,0.7407407407407407
balancedtree-t32-s42-l32-b2,32,32,DNA,0.48,0.4,0.6
balancedtree-t32-s42-l128-b2,32,128,DNA,0.847457627118644,0.8333333333333334,0.8620689655172413
balancedtree-t32-s42-l16-b2,32,16,DNA,0.11764705882352941,0.06666666666666667,0.5
balancedtree-t32-s42-l256-b2,32,256,DNA,0.6785714285714285,0.6333333333333333,0.7307692307692307
balancedtree-t32-s42-l32-b2,32,32,DNA,0.4897959183673469,0.4,0.631578947368421
balancedtree-t32-s42-l512-b2,32,512,DNA,0.689655172413793,0.6666666666666666,0.7142857142857143
balancedtree-t32-s42-l64-b2,32,64,DNA,0.8070175438596491,0.7666666666666667,0.8518518518518519
balancedtree-t512-s42-l1024-b2,512,1024,DNA,0.7750511247443763,0.7431372549019608,0.8098290598290598
balancedtree-t512-s42-l128-b2,512,128,DNA,0.7037815126050421,0.6568627450980392,0.7579185520361991
balancedtree-t512-s42-l16-b2,512,16,DNA,0.06972477064220182,0.03725490196078431,0.5428571428571428
balancedtree-t512-s42-l256-b2,512,256,DNA,0.7585492227979276,0.7176470588235294,0.8043956043956044
balancedtree-t512-s42-l32-b2,512,32,DNA,0.3267175572519084,0.20980392156862746,0.7379310344827587
balancedtree-t512-s42-l512-b2,512,512,DNA,0.790224032586558,0.7607843137254902,0.8220338983050848
balancedtree-t512-s42-l64-b2,512,64,DNA,0.6079295154185023,0.5411764705882353,0.6934673366834171
balancedtree-t64-s42-l1024-b2,64,1024,DNA,0.8333333333333334,0.8064516129032258,0.8620689655172413
balancedtree-t64-s42-l128-b2,64,128,DNA,0.7731092436974789,0.7419354838709677,0.8070175438596491
balancedtree-t64-s42-l16-b2,64,16,DNA,0.08333333333333333,0.04838709677419355,0.3
balancedtree-t512-s42-l1024-b2,512,1024,DNA,0.7816326530612245,0.7509803921568627,0.8148936170212766
balancedtree-t512-s42-l128-b2,512,128,DNA,0.70042194092827,0.6509803921568628,0.7579908675799086
balancedtree-t512-s42-l16-b2,512,16,DNA,0.08775137111517366,0.047058823529411764,0.6486486486486487
balancedtree-t512-s42-l256-b2,512,256,DNA,0.7587628865979382,0.7215686274509804,0.8
balancedtree-t512-s42-l32-b2,512,32,DNA,0.3476968796433878,0.22941176470588234,0.7177914110429447
balancedtree-t512-s42-l512-b2,512,512,DNA,0.7926455566905004,0.7607843137254902,0.8272921108742004
balancedtree-t512-s42-l64-b2,512,64,DNA,0.6083150984682713,0.5450980392156862,0.6881188118811881
balancedtree-t64-s42-l1024-b2,64,1024,DNA,0.7966101694915255,0.7580645161290323,0.8392857142857143
balancedtree-t64-s42-l128-b2,64,128,DNA,0.7796610169491526,0.7419354838709677,0.8214285714285714
balancedtree-t64-s42-l16-b2,64,16,DNA,0.11267605633802817,0.06451612903225806,0.4444444444444444
balancedtree-t64-s42-l256-b2,64,256,DNA,0.7457627118644068,0.7096774193548387,0.7857142857142857
balancedtree-t64-s42-l32-b2,64,32,DNA,0.5200000000000001,0.41935483870967744,0.6842105263157895
balancedtree-t64-s42-l512-b2,64,512,DNA,0.8099173553719008,0.7903225806451613,0.8305084745762712
balancedtree-t64-s42-l64-b2,64,64,DNA,0.5384615384615384,0.45161290322580644,0.6666666666666666
balancedtree-t64-s42-l32-b2,64,32,DNA,0.5576923076923077,0.46774193548387094,0.6904761904761905
balancedtree-t64-s42-l512-b2,64,512,DNA,0.8166666666666667,0.7903225806451613,0.8448275862068966
balancedtree-t64-s42-l64-b2,64,64,DNA,0.5436893203883495,0.45161290322580644,0.6829268292682927
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