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Major update of MixMHC2pred towards version 2.0.RC
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# License file in word format.
License.docx

# Compiled object files
*.o
bin/**

# Makefile is in bin folder but should be included
!bin/Makefile
6,865 changes: 6,858 additions & 7 deletions Alleles_list.txt
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36 changes: 21 additions & 15 deletions FAQ.md
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## What kind of predictions can I make with MixMHC2pred

MixMHC2pred is a predictor of HLA-II ligand displayed at the cell surface.
It combines predictions of affinity to HLA-II molecules including
binding core offset preferences, as well as peptide N-/C-terminal motifs and
peptide length preference (which are likely emerging from the peptide
processing steps).
MixMHC2pred is a predictor of MHC-II ligands displayed at the cell surface.
It combines predictions of affinity to MHC-II molecules together with other
features linked to antigen processing and presentation. It can work for any
human MHC-II allele (HLA-DR/-DP/-DQ) as well as for many mouse, cattle and
chicken alleles.

Peptides ranking high in MixMHC2pred predictions are more likely to elicit
CD4+ T cell recognition.

## How should I interpret the output of MixMHC2pred

* *Peptide* gives the sequence of the peptides, in the same order as
provided in input.
* *Peptide* and *Context* give the sequence of the peptides (respectively
context), in the same order as provided in input.
* *BestAllele* gives the name of the best allele (based
on the allele with best predicted score for the given peptide).
* *%Rank_...* give the predicted score for the best allele and separately for
each allele asked. The score is given as a percentile rank (i.e., the
percent of random peptides that would have a score higher than the peptide
provided in input among peptides of sizes 12-25 amino acids; best score is
provided in input among peptides of sizes 12-21 amino acids; best score is
about 0, worst score is 100).
* *%Rank_best_perL* is similar to *%Rank_best* but computed based only on peptides
having the same length than the given peptide. This score thus doesn't follow
the length distribution observed in naturally presented ligands.
* *Core_best* indicates the best predicted core binding sequence for each
peptide towards its best allele.
* *CoreP1_...* give the most likely binding core position for the given peptide
towards the allele (this tells the position of the first amino acid from the
binding core (which has a size of 9 aa in the predictions), starting at a
value of 1 (i.e. if binding core corresponds to the 9 first amino acids
from the peptide, this *CoreP1 = 1*)).
* *subSpec_...* tell in which sub-specificity the given peptide
is likely bound toward the given allele. The value *1* corresponds to the
main sub-specificity (the only one for multiple alleles). But for example
for *DRB1\*08:01* allele a 2nd sub-specificity exists and is indicated by the
value *2*. For alleles accomodating reverse binding, a value of *-1* indicates
that the given peptide is bound in the reverse orientation.

Peptides that are too short (less than 12 amino acids), too long (more than
25 amino acids) or that contain non standard amino acids have *NA* values
21 amino acids) or that contain non standard amino acids have *NA* values
instead of their scores.

## How can I rank my peptides based on MixMHC2pred predictions
Expand All @@ -59,7 +62,10 @@ that is causing the issue.

If you are using MixMHC2pred, please refer to

Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif
deconvolution of immunopeptidomes. *Nat. Biotechnol.* 37, 1283–1286 (2019).
Racle, J., et al., Accurate predictions of MHC-II specificities (in prep.).

and

It is available [here](https://www.nature.com/articles/s41587-019-0289-6).
Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif
deconvolution of immunopeptidomes. *Nat. Biotechnol.* 37, 1283–1286 (2019)
(available [here](https://www.nature.com/articles/s41587-019-0289-6)).
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4 changes: 2 additions & 2 deletions LICENSE
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Expand Up @@ -8,7 +8,7 @@ WHEREAS, LICENSEE desires to license the PROGRAM and LICR desires to grant a lic
NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:

1. DEFINITIONS
1.1 PROGRAM shall mean the source code known as MixMHC2pred (version 1.2), as it exists on the EFFECTIVE DATE.
1.1 PROGRAM shall mean the source code known as MixMHC2pred (version 2.0), as it exists on the EFFECTIVE DATE.

2. LICENSE
2.1 Grant. Subject to the terms of this Agreement, LICR hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM. LICENSEE hereby automatically grants to LICR a non-exclusive, royalty-free, irrevocable license to any LICENSEE bug fixes or modifications to the PROGRAM with unlimited rights to sublicense and/or distribute. LICENSEE agrees to provide any such modifications and bug fixes to LICR promptly upon their creation.
Expand All @@ -17,7 +17,7 @@ The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other th
2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of LICR, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
3. OWNERSHIP OF INTELLECTUAL PROPERTY
LICENSEE acknowledges that title to the PROGRAM shall remain with LICR. The PROGRAM shall be marked with the notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
Notice of attribution: The MixMHC2pred (version 1.2) program was made available through the generosity of Ludwig Institute for Cancer Research Ltd.
Notice of attribution: The MixMHC2pred (version 2.0) program was made available through the generosity of Ludwig Institute for Cancer Research Ltd.
LICENSEE shall not use any trademark or trade name of LICR, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of LICR except as states above for attribution purposes.

4. INDEMNIFICATION
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9 changes: 9 additions & 0 deletions NEWS
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Release notes from MixMHC2pred
========================================================================

Version 2.0.RC (10.06.2022)
* Major update of MixMHC2pred, allowing for pan-allele predictions for human and
non-human MHC-II alleles.
* Implementation vastly changed; it is now based on multiple neural networks and
it was trained on a much larger MHC-II peptidomics dataset.
* Please note that the format of the input and output files have changed, as
well as the available input arguments.


Version 1.2 (03.02.2020)
------------------------------------------------------------------------
* Output contains now also the individual predictions from each allele in
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47 changes: 47 additions & 0 deletions PWMdef/BoLA_DRB3_001_01.txt
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Allele BoLA_DRB3_001_01
Type Standard
n_specificities 1
npep_u 1
npep_t 2278
spec_ids 1
L_core 9
L_N 0
L_C 0
CS_perL 1
pepL_lower 12
pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.0656 1.5795 1.8272 3.6352 0.6065 0.7169 1.8821 1.1606 0.1027
C 0.08 0.0478 0.0514 0.0609 0.0461 0.0453 0.0491 0.0463 0.0336
D 0.0288 0.6859 0.1757 1.0529 0.8465 0.2619 0.4368 0.4484 0.0598
E 0.0233 2.0149 0.6167 0.0494 1.2981 0.3221 0.5774 0.8458 0.1291
F 1.9068 0.8098 1.0319 0.8521 0.392 0.1181 1.0758 0.4964 0.8703
G 0.0346 0.5059 0.528 0.3518 0.6197 0.084 1.9559 0.888 0.1635
H 0.0326 1.6558 1.138 3.8821 1.5202 1.8738 1.3601 1.4894 0.066
I 6.9017 0.7769 2.2768 0.5221 1.4503 1.8748 0.6924 1.3573 0.2428
K 0.0353 1.1537 1.1118 0.1256 2.4476 3.9994 1.3362 2.2131 9.9038
L 3.2387 0.4957 0.7391 0.1269 1.1303 0.9301 1.0556 1.1283 0.3037
M 0.9413 0.3504 0.8451 0.0689 0.7533 0.5119 0.6703 0.1151 0.3991
N 0.0351 1.425 0.7444 1.2223 0.6257 0.6249 0.7859 0.7058 0.084
P 0.1387 0.0627 0.8781 0.1048 0.466 0.147 0.586 1.2445 0.0302
Q 0.0772 1.3477 0.9685 0.0976 1.1145 0.6921 0.4842 1.1465 0.0788
R 0.031 1.0439 0.713 0.0488 1.3626 3.4402 1.235 1.5223 4.1681
S 0.0266 1.0177 1.0253 2.5776 0.3476 0.128 0.8726 0.6997 0.051
T 0.1557 1.5804 0.6213 1.9623 0.9794 0.851 0.9955 0.6788 0.1008
V 3.9282 1.1535 1.341 1.8408 1.8777 2.0227 0.5685 0.8851 0.337
W 0.0825 0.0435 0.6387 0.0389 0.2474 0.0383 1.3904 0.0759 1.2142
Y 0.5871 1.1289 3.3362 0.0892 0.6191 0.0797 1.6228 1.0304 1.0469

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
47 changes: 47 additions & 0 deletions PWMdef/BoLA_DRB3_001_03.txt
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Allele BoLA_DRB3_001_03
Type Standard
n_specificities 1
npep_u 1
npep_t 5000
spec_ids 1
L_core 9
L_N 0
L_C 0
CS_perL 1
pepL_lower 12
pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1465 1.4655 1.6064 3.2247 0.7226 0.6129 1.2577 1.1812 0.194
C 0.0713 0.1005 0.1842 0.1696 0.088 0.102 0.2619 0.116 0.0546
D 0.0594 0.6538 0.2739 1.0039 0.8378 0.5374 0.5804 0.5499 0.0818
E 0.047 1.7354 0.6463 0.173 1.2419 0.3235 1.2669 0.9164 0.1446
F 1.8604 0.7927 1.3955 0.8709 0.4796 0.1725 0.9863 0.6052 0.7831
G 0.0707 0.46 0.5172 0.502 0.6401 0.1693 0.8959 0.9468 0.1863
H 0.0614 1.5931 1.0273 3.7008 1.3412 1.589 1.1646 1.5282 0.1647
I 7.2072 0.9289 2.1104 0.606 1.4051 1.5996 0.9942 1.0162 0.2735
K 0.0495 1.1939 0.9458 0.1554 2.289 4.498 0.9144 1.5537 9.2261
L 2.9731 0.6749 0.8213 0.1882 1.0476 0.8571 1.4551 1.0855 0.3493
M 1.3263 0.4812 1.171 0.1542 0.7469 0.514 0.9297 0.5538 0.578
N 0.0484 1.3847 0.7754 1.369 0.7344 0.7587 1.5932 0.9038 0.151
P 0.1101 0.0719 1.1215 0.1192 0.5616 0.3364 0.6369 1.2759 0.039
Q 0.0497 1.2558 1.0606 0.2154 1.1306 0.6616 0.9695 1.0813 0.163
R 0.0436 1.2263 0.663 0.1 1.3004 2.9351 0.6964 1.4304 4.3748
S 0.0441 0.96 0.9522 2.416 0.4621 0.2675 0.7842 0.746 0.1195
T 0.1397 1.4589 0.6026 1.9738 1.0057 0.8711 0.7388 0.863 0.1106
V 3.7624 1.2283 1.3626 1.7616 1.7657 1.6845 1.0993 0.997 0.3469
W 0.4394 0.3642 0.9519 0.199 0.3143 0.1182 0.8476 0.3334 0.6464
Y 0.6058 1.2166 2.6351 0.1474 0.7234 0.176 1.4858 1.0766 1.0786

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
47 changes: 47 additions & 0 deletions PWMdef/BoLA_DRB3_002_01.txt
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Allele BoLA_DRB3_002_01
Type Standard
n_specificities 1
npep_u 1
npep_t 5000
spec_ids 1
L_core 9
L_N 0
L_C 0
CS_perL 1
pepL_lower 12
pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1391 0.9786 1.5907 0.5882 1.0627 0.3353 1.0604 1.1812 1.092
C 0.0583 0.1182 0.2804 0.1561 0.1722 0.0273 0.28 0.116 0.542
D 0.0402 0.5555 0.5111 0.3207 1.3732 0.2206 0.9503 0.5499 0.1885
E 0.0321 1.1065 0.795 0.3496 1.1806 0.2015 1.3143 0.9164 0.2375
F 0.8712 0.8442 1.0454 4.8675 0.4956 0.0511 0.9596 0.6052 1.4774
G 0.0626 0.3341 0.7087 0.1811 0.7015 0.1031 0.8136 0.9468 0.4496
H 0.041 1.4506 0.8247 2.3532 1.2293 1.1755 1.34 1.5282 0.3514
I 8.7661 1.5874 2.3246 1.4751 0.9375 0.5336 1.2289 1.0162 1.9125
K 0.0339 1.7251 0.8812 0.7418 1.7439 8.5146 0.8889 1.5537 0.212
L 2.7494 0.856 0.9193 0.8987 0.4537 0.2268 0.8165 1.0855 2.2623
M 1.3964 0.5286 1.1058 1.3633 0.634 0.1342 1.0087 0.5538 1.4762
N 0.0398 1.0179 0.8488 1.1157 1.1752 0.253 1.9542 0.9038 0.6783
P 0.0759 0.0529 1.0026 0.0635 1.1399 0.1812 0.7904 1.2759 0.1227
Q 0.0349 1.1967 0.8584 0.7749 1.2348 0.3052 1.2106 1.0813 0.55
R 0.0305 1.746 0.7923 0.6435 1.1435 4.645 0.6144 1.4304 0.375
S 0.033 0.7128 0.7845 0.2884 0.9813 0.1256 0.8682 0.746 0.6773
T 0.1218 1.1169 0.8781 0.4386 1.3604 0.4821 0.8502 0.863 0.8719
V 3.9808 1.9381 1.4068 1.0444 0.8719 0.5979 1.1176 0.997 3.0834
W 0.1798 0.5113 0.5362 5.8232 0.3946 0.0396 0.8161 0.3334 0.2168
Y 0.1653 1.1473 1.7551 5.5436 0.9295 0.0692 1.5865 1.0766 2.7968

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
47 changes: 47 additions & 0 deletions PWMdef/BoLA_DRB3_002_02.txt
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Allele BoLA_DRB3_002_02
Type Standard
n_specificities 1
npep_u 1
npep_t 5000
spec_ids 1
L_core 9
L_N 0
L_C 0
CS_perL 1
pepL_lower 12
pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.1391 0.9786 1.5907 0.5882 1.0627 0.3353 1.0604 1.1812 1.092
C 0.0583 0.1182 0.2804 0.1561 0.1722 0.0273 0.28 0.116 0.542
D 0.0402 0.5555 0.5111 0.3207 1.3732 0.2206 0.9503 0.5499 0.1885
E 0.0321 1.1065 0.795 0.3496 1.1806 0.2015 1.3143 0.9164 0.2375
F 0.8712 0.8442 1.0454 4.8675 0.4956 0.0511 0.9596 0.6052 1.4774
G 0.0626 0.3341 0.7087 0.1811 0.7015 0.1031 0.8136 0.9468 0.4496
H 0.041 1.4506 0.8247 2.3532 1.2293 1.1755 1.34 1.5282 0.3514
I 8.7661 1.5874 2.3246 1.4751 0.9375 0.5336 1.2289 1.0162 1.9125
K 0.0339 1.7251 0.8812 0.7418 1.7439 8.5146 0.8889 1.5537 0.212
L 2.7494 0.856 0.9193 0.8987 0.4537 0.2268 0.8165 1.0855 2.2623
M 1.3964 0.5286 1.1058 1.3633 0.634 0.1342 1.0087 0.5538 1.4762
N 0.0398 1.0179 0.8488 1.1157 1.1752 0.253 1.9542 0.9038 0.6783
P 0.0759 0.0529 1.0026 0.0635 1.1399 0.1812 0.7904 1.2759 0.1227
Q 0.0349 1.1967 0.8584 0.7749 1.2348 0.3052 1.2106 1.0813 0.55
R 0.0305 1.746 0.7923 0.6435 1.1435 4.645 0.6144 1.4304 0.375
S 0.033 0.7128 0.7845 0.2884 0.9813 0.1256 0.8682 0.746 0.6773
T 0.1218 1.1169 0.8781 0.4386 1.3604 0.4821 0.8502 0.863 0.8719
V 3.9808 1.9381 1.4068 1.0444 0.8719 0.5979 1.1176 0.997 3.0834
W 0.1798 0.5113 0.5362 5.8232 0.3946 0.0396 0.8161 0.3334 0.2168
Y 0.1653 1.1473 1.7551 5.5436 0.9295 0.0692 1.5865 1.0766 2.7968

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
47 changes: 47 additions & 0 deletions PWMdef/BoLA_DRB3_003_01.txt
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Allele BoLA_DRB3_003_01
Type Standard
n_specificities 1
npep_u 1
npep_t 5000
spec_ids 1
L_core 9
L_N 0
L_C 0
CS_perL 1
pepL_lower 12
pepL_upper 21
n_diff_aa 20

PWM_norm.1 P1 P2 P3 P4 P5 P6 P7 P8 P9
A 0.0934 0.9786 1.4683 1.1293 0.9304 2.5989 0.9289 1.1812 0.9352
C 0.049 0.1182 0.3474 0.2577 0.2937 0.2749 0.181 0.116 0.5129
D 0.0361 0.5555 0.4121 1.9061 1.0494 0.513 0.9071 0.5499 0.2342
E 0.0576 1.1065 0.6688 0.7839 1.0349 0.8162 1.2776 0.9164 0.2369
F 8.2964 0.8442 1.1583 0.3547 0.6803 0.4056 0.469 0.6052 1.1142
G 0.0619 0.3341 0.6012 0.7662 0.9066 1.2411 0.9229 0.9468 0.3379
H 0.1244 1.4506 0.8028 0.4577 1.3764 0.3803 0.9597 1.5282 0.3055
I 2.7704 1.5874 2.2495 0.6114 0.88 1.4893 1.2378 1.0162 1.8667
K 0.0618 1.7251 0.9267 0.2101 1.573 0.0999 0.5508 1.5537 0.2538
L 1.3527 0.856 0.9042 0.4972 0.6022 0.7256 0.7632 1.0855 2.5009
M 0.9209 0.5286 1.3498 0.5831 0.8672 0.5703 0.4483 0.5538 1.4184
N 0.0713 1.0179 0.915 8.7352 1.2193 1.9808 2.7384 0.9038 0.9454
P 0.0388 0.0529 1.1054 0.1232 1.4207 1.3218 1.6597 1.2759 0.1017
Q 0.0536 1.1967 0.9109 1.1762 1.1273 1.3504 1.3531 1.0813 0.4646
R 0.0379 1.746 0.8265 0.1932 1.1305 0.1 0.4304 1.4304 0.4499
S 0.0414 0.7128 0.8742 1.1615 0.9185 0.7966 0.7061 0.746 0.6047
T 0.0773 1.1169 0.8169 0.9636 1.2222 1.1279 1.1622 0.863 0.8281
V 0.9818 1.9381 1.4084 0.7256 0.8829 1.8376 1.358 0.997 3.2316
W 4.5203 0.5113 0.748 0.2846 0.6652 0.0888 0.4495 0.3334 0.2579
Y 10.5593 1.1473 1.7927 0.2256 0.8134 0.213 0.8112 1.0766 2.7484

pepL alpha w_s
12 99.5307 0.083 0.1488 0 0.3949 0.3734
13 98.9575 0.0263 0.0764 0.2382 0.4675 0.1916
14 98.3294 0.0043 0.0259 0.161 0 0.4702 0.2977 0.0409
15 98.0139 0.0017 0.0096 0.0839 0.376 0.4093 0.0998 0.0197
16 98.2233 8e-04 0.0022 0.03 0.2337 0 0.5219 0.1563 0.0471 0.0079
17 98.735 8e-04 0.0019 0.0146 0.1152 0.4293 0.2806 0.114 0.0363 0.0072
18 99.2174 5e-04 0.0013 0.0066 0.0433 0.2908 0 0.3312 0.218 0.0767 0.0267 0.005
19 99.5133 0.001 0.0012 0.0074 0.029 0.145 0.2323 0.2918 0.1844 0.0762 0.0263 0.0055
20 99.691 0.001 0.0012 0.0048 0.0176 0.0704 0.1449 0 0.2809 0.2454 0.1596 0.0505 0.0192 0.0045
21 99.7886 0.0013 0.002 0.0054 0.0189 0.0569 0.1038 0.1383 0.2554 0.2215 0.1327 0.043 0.0166 0.0041
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