-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
9256867
commit 57fd509
Showing
12 changed files
with
13,564 additions
and
9,743 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -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: | ||
``` | ||
|
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 | ||
balancedtree-t16-s42-l1024-b2,16,1024,DNA,0.7407407407407408,0.7142857142857143,0.7692307692307693 | ||
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 | ||
balancedtree-t128-s42-l16-b2,128,16,DNA,0.04511278195488722,0.023809523809523808,0.42857142857142855 | ||
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 | ||
balancedtree-t16-s42-l512-b2,16,512,DNA,0.64,0.5714285714285714,0.7272727272727273 | ||
balancedtree-t16-s42-l32-b2,16,32,DNA,0.64,0.5714285714285714,0.7272727272727273 | ||
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 |
Oops, something went wrong.