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valdeanda committed Aug 19, 2019
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6 changes: 6 additions & 0 deletions config/config.txt
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Cycle Path Comple Input Genes Input Genomes Domains AUC Score(FDR0.1) Score(FDR0.01) Score(FDR0.001) Score(FDR0.0001)
sulfur cycles/sulfur/ cycles/sulfur/pfam2kegg.tab 152 161 112 0.985 4.156 8.049 10.816 12.285
carbon cycles/carbon/ cycles/carbon/pfam2kegg.tab 135 90 119 0.988 9.735 18.744 34.26 34.908
oxygen cycles/oxygen/ 50 53 55 0.983 5.098 7.288 8.155 8.247
iron cycles/iron/ cycles/iron/pfam2kegg.tab 36 34 112 0.863 7.412 9.571 10.241 10.322
nitrogen cycles/nitrogen/ cycles/nitrogen/pfam2kegg.tab 267 144 176 0.791 15.974 17.7 18.785 19.03
1,372 changes: 1,372 additions & 0 deletions cycles/carbon/carbon.fasta
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90 changes: 90 additions & 0 deletions cycles/carbon/carbon.txt
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GCF_000006175.1 Methanococcus voltae A3
GCF_000007065.1 Methanosarcina mazei Go1
GCF_000007345.1 Methanosarcina acetivorans C2A
GCF_000008325.1 Methylococcus capsulatus str. Bath
GCF_000008645.1 Methanothermobacter thermautotrophicus str. Delta H
GCF_000011585.1 Methanococcus maripaludis S2
GCF_000012545.1 Methanosphaera stadtmanae DSM 3091
GCF_000013445.1 Methanospirillum hungatei JF-1
GCF_000013705.1 Methylobacillus flagellatus KT
GCF_000013725.1 Methanococcoides burtonii DSM 6242
GCF_000015725.1 Methylibium petroleiphilum PM1
GCF_000015765.1 Methanocorpusculum labreanum Z
GCF_000015825.1 Methanoculleus marisnigri JR1
GCF_000016125.1 Methanococcus maripaludis C5
GCF_000016525.1 Methanobrevibacter smithii ATCC 35061
GCF_000017165.1 Methanococcus vannielii SB
GCF_000017185.1 Methanococcus aeolicus Nankai-3
GCF_000017225.1 Methanococcus maripaludis C7
GCF_000017625.1 Methanoregula boonei 6A8
GCF_000018485.1 Methanococcus maripaludis C6
GCF_000018845.1 Methylobacterium extorquens PA1
GCF_000019365.1 Methylobacterium sp. 4-46
GCF_000019665.1 Methylacidiphilum infernorum V4
GCF_000019725.1 Methylobacterium radiotolerans JCM 2831
GCF_000019945.1 Methylobacterium populi BJ001
GCF_000021745.1 Methylocella silvestris BL2
GCF_000021965.1 Methanosphaerula palustris E1-9c
GCF_000022085.1 Methylobacterium nodulans ORS 2060
GCF_000023705.1 Methylotenera mobilis JLW8
GCF_000023745.1 Methylovorus glucosetrophus SIP3-4
GCF_000023985.1 Methanocaldococcus fervens AG86
GCF_000024185.1 Methanobrevibacter ruminantium M1
GCF_000024625.1 Methanocaldococcus vulcanius M7
GCF_000025525.1 Methanocaldococcus sp. FS406-22
GCF_000025865.1 Methanohalophilus mahii DSM 5219
GCF_000063445.1 Methanocella arvoryzae MRE50
GCF_000091665.1 Methanocaldococcus jannaschii DSM 2661
GCF_000092305.1 Methanocaldococcus infernus ME
GCF_000093025.1 Methylotenera versatilis 301
GCF_000145295.1 Methanothermobacter marburgensis str. Marburg
GCF_000147875.1 Methanolacinia petrolearia DSM 11571
GCF_000166095.1 Methanothermus fervidus DSM 2088
GCF_000179575.2 Methanothermococcus okinawensis IH1
GCF_000191585.1 Methanobacterium lacus
GCF_000195895.1 Methanosarcina barkeri str. Fusaro
GCF_000196655.1 Methanohalobium evestigatum Z-7303
GCF_000204415.1 Methanosaeta concilii GP6
GCF_000214415.1 Methanotorris igneus Kol 5
GCF_000214665.1 Methylomonas methanica MC09
GCF_000214725.1 Methanobacterium paludis
GCF_000217995.1 Methanosalsum zhilinae DSM 4017
GCF_000235565.1 Methanosaeta harundinacea 6Ac
GCF_000235685.2 Methanolinea tarda NOBI-1
GCF_000251105.1 Methanocella conradii HZ254
GCF_000260965.1 Methylophaga frappieri
GCF_000260985.3 Methylophaga nitratireducenticrescens
GCF_000300255.2 Candidatus Methanomethylophilus alvus Mx1201
GCF_000304315.1 Methylocystis sp. SC2
GCF_000304355.2 Methanoculleus bourgensis MS2
GCF_000306725.1 Methanolobus psychrophilus R15
GCF_000327485.1 Methanoregula formicica SMSP
GCF_000328665.1 Methanomethylovorans hollandica DSM 15978
GCF_000404165.1 Methanobrevibacter sp. AbM4
GCF_000404225.1 Candidatus Methanomassiliicoccus intestinalis Issoire-Mx1
GCF_000499765.1 Methanobacterium sp. MB1
GCF_000739065.1 Methanocaldococcus bathoardescens
GCF_000762265.1 Methanobacterium formicicum
GCF_000785705.2 Methylomonas denitrificans
GCF_000800805.1 Candidatus Methanoplasma termitum
GCF_000828475.1 Methyloceanibacter caenitepidi
GCF_000828575.1 Methanothermobacter sp. CaT2
GCF_000953015.1 Candidatus Methylopumilus turicensis
GCF_000953475.1 Methylacidiphilum fumariolicum SolV
GCF_000968535.2 Methylomicrobium alcaliphilum 20Z
GCF_000969885.1 Methanosarcina thermophila TM-1
GCF_000969905.1 Methanosarcina vacuolata Z-761
GCF_000969965.1 Methanosarcina sp. WWM596
GCF_000970025.1 Methanosarcina barkeri MS
GCF_000970045.1 Methanosarcina sp. MTP4
GCF_000970085.1 Methanosarcina siciliae T4/M
GCF_000970265.1 Methanosarcina lacustris Z-7289
GCF_000970285.1 Methanosarcina horonobensis HB-1 = JCM 15518
GCF_000970305.1 Methanosarcina barkeri 3
GCF_000970325.1 Methanococcoides methylutens MM1
GCF_000981505.1 Candidatus Methylopumilus planktonicus
GCF_001183865.1 Methylophilus sp. TWE2
GCF_001477655.1 Methanobrevibacter millerae
GCF_001542815.1 Methylobacterium sp. AMS5
GCF_001548015.1 Methylobacterium aquaticum
GCF_001644685.1 Methylomonas sp. DH-1
120 changes: 120 additions & 0 deletions cycles/carbon/entropies.tab
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real 30 60 100 150 200 250 300
PF00037 0.088 0.107 0.090 0.086 0.085 0.085 0.088 0.087
PF00067 -0.166 -0.084 -0.142 -0.162 -0.165 -0.165 -0.166 -0.165
PF00115 -0.372 -0.201 -0.371 -0.371 -0.371 -0.372 -0.372 -0.372
PF00116 -0.330 -0.144 -0.275 -0.327 -0.335 -0.335 -0.335 -0.330
PF00117 0.008 0.036 0.012 0.008 0.008 0.008 0.008 0.008
PF00120 0.093 0.213 0.137 0.102 0.096 0.093 0.093 0.093
PF00142 0.094 1.293 0.359 0.294 0.310 0.244 0.114 0.100
PF00146 0.442 -0.033 0.446 0.432 0.436 0.440 0.440 0.440
PF00148 1.799 0.869 1.672 1.760 1.793 1.757 1.793 1.799
PF00173 0.404 0.386 0.435 0.418 0.420 0.406 0.409 0.411
PF00174 0.030 -0.023 -0.001 0.016 0.015 0.014 0.014 0.014
PF00175 0.124 -0.034 -0.217 0.124 0.131 0.137 0.124 0.124
PF00194 -0.061 -0.063 -0.060 -0.060 -0.060 -0.060 -0.060 -0.060
PF00208 -0.155 -0.281 -0.151 -0.162 -0.168 -0.156 -0.159 -0.157
PF00296 0.491 0.377 0.483 0.495 0.491 0.490 0.490 0.489
PF00310 0.186 -0.276 0.043 0.120 0.140 0.101 0.121 0.179
PF00329 -0.030 -0.036 -0.011 -0.007 -0.025 -0.029 -0.044 -0.029
PF00346 0.463 0.220 0.468 0.464 0.465 0.465 0.463 0.463
PF00361 0.285 0.006 0.250 0.285 0.285 0.286 0.285 0.285
PF00374 1.037 0.562 0.996 1.047 1.030 1.030 1.003 1.027
PF00384 0.302 0.146 0.100 0.249 0.311 0.307 0.304 0.302
PF00420 0.152 0.213 0.171 0.169 0.169 0.152 0.152 0.152
PF00441 -0.351 -0.262 -0.337 -0.348 -0.355 -0.350 -0.351 -0.351
PF00484 -0.056 -0.160 -0.065 -0.055 -0.056 -0.056 -0.056 -0.056
PF00499 -0.117 -0.005 -0.119 -0.115 -0.117 -0.117 -0.117 -0.117
PF00507 -0.140 -0.120 -0.135 -0.140 -0.140 -0.140 -0.140 -0.140
PF00662 -0.074 -0.141 -0.061 -0.073 -0.025 -0.052 -0.061 -0.041
PF00696 0.002 0.156 0.004 0.002 0.002 0.002 0.002 0.002
PF00795 -0.150 0.015 -0.108 -0.133 -0.141 -0.145 -0.148 -0.148
PF00871 -0.344 -0.351 -0.349 -0.339 -0.344 -0.344 -0.344 -0.344
PF00970 -0.319 -0.023 -0.185 -0.281 -0.309 -0.328 -0.322 -0.320
PF00988 0.159 0.226 0.161 0.163 0.160 0.161 0.159 0.159
PF01011 0.390 0.555 0.439 0.404 0.390 0.404 0.438 0.367
PF01058 0.483 0.487 0.489 0.483 0.483 0.483 0.483 0.484
PF01077 0.328 0.341 0.363 0.315 0.333 0.331 0.331 0.328
PF01208 -0.005 -0.270 -0.102 -0.090 -0.085 -0.036 -0.038 -0.004
PF01266 0.028 -0.197 -0.126 -0.163 -0.012 0.029 0.018 0.018
PF01493 0.447 0.501 0.800 0.669 0.636 0.612 0.625 0.584
PF01515 -0.261 -0.368 -0.402 -0.394 -0.303 -0.247 -0.255 -0.252
PF01568 0.431 0.439 0.568 0.478 0.501 0.474 0.457 0.449
PF01571 -0.408 -0.369 -0.392 -0.402 -0.404 -0.408 -0.408 -0.409
PF01645 0.166 0.349 0.180 0.111 0.093 0.099 0.137 0.150
PF01913 3.647 3.647 3.626 3.606 3.587 3.626 3.647 3.647
PF01993 2.876 2.876 2.876 2.876 2.876 2.876 2.876 2.876
PF02007 2.600 2.844 2.709 2.639 2.435 2.449 2.402 2.468
PF02142 0.099 -0.128 -0.067 -0.095 -0.016 -0.067 -0.059 -0.012
PF02239 0.368 -0.016 0.044 0.449 0.448 0.395 0.405 0.353
PF02240 3.168 3.168 3.168 3.168 3.168 3.168 3.168 3.168
PF02241 3.168 3.168 3.168 3.168 3.168 3.168 3.168 3.168
PF02249 3.168 2.915 3.168 3.168 3.168 3.168 3.168 3.168
PF02289 3.353 3.353 3.353 3.353 3.353 3.353 3.353 3.353
PF02315 0.811 0.811 0.811 0.811 0.811 0.811 0.811 0.811
PF02335 -0.064 -0.031 -0.037 -0.064 -0.070 -0.070 -0.074 -0.075
PF02461 0.275 0.275 0.275 0.275 0.275 0.275 0.275 0.275
PF02552 1.491 1.956 1.499 1.160 1.143 1.129 1.207 1.258
PF02560 0.097 0.098 0.098 0.098 0.098 0.098 0.098 0.098
PF02663 1.642 1.843 1.753 1.744 1.658 1.642 1.646 1.642
PF02665 -0.040 -0.104 -0.053 0.113 0.063 -0.036 -0.073 -0.046
PF02741 3.647 3.549 3.647 3.647 3.647 3.647 3.647 3.647
PF02745 3.168 3.168 3.168 3.168 3.168 3.168 3.168 3.168
PF02771 -0.356 -0.267 -0.337 -0.347 -0.352 -0.350 -0.351 -0.355
PF02783 3.168 3.168 3.168 3.168 3.168 3.168 3.168 3.168
PF02786 0.044 0.081 0.057 0.049 0.044 0.042 0.042 0.043
PF02787 0.141 0.040 0.178 0.066 0.073 0.104 0.148 0.110
PF02812 -0.340 -0.282 -0.337 -0.335 -0.338 -0.340 -0.340 -0.340
PF02975 0.020 0.020 0.020 0.020 0.020 0.020 0.020 0.020
PF03060 0.058 -0.194 -0.039 0.020 0.082 0.145 0.148 0.146
PF03063 0.937 0.886 0.937 0.937 0.935 0.937 0.937 0.937
PF03069 -0.089 -0.065 -0.087 -0.090 -0.091 -0.090 -0.089 -0.089
PF03139 0.158 0.158 0.158 0.158 0.158 0.158 0.158 0.158
PF03201 1.298 1.248 1.298 1.283 1.283 1.298 1.298 1.298
PF03404 -0.030 -0.007 -0.019 -0.044 -0.039 -0.021 -0.029 -0.029
PF03460 0.323 0.328 0.290 0.316 0.326 0.326 0.323 0.324
PF03598 1.881 1.845 1.893 1.902 1.841 1.888 1.881 1.881
PF03599 1.227 2.074 1.794 1.502 1.246 1.121 1.081 1.097
PF03951 0.189 0.081 0.224 0.243 0.190 0.189 0.229 0.201
PF04060 0.958 1.037 0.927 1.025 0.976 0.971 0.998 0.964
PF04206 3.032 3.032 3.032 3.032 3.032 3.032 3.032 3.032
PF04207 3.032 3.032 3.032 3.032 3.032 3.032 3.032 3.032
PF04208 2.898 2.941 2.898 2.898 2.898 2.898 2.898 2.898
PF04210 2.970 3.001 2.847 2.792 2.844 2.941 2.985 2.970
PF04211 3.032 2.982 3.032 3.032 3.032 3.032 3.032 3.032
PF04267 0.002 0.002 0.002 0.003 0.004 0.003 0.003 0.003
PF04268 -0.191 -0.045 -0.029 -0.125 -0.185 -0.210 -0.206 -0.198
PF04324 -0.306 -0.233 -0.284 -0.299 -0.307 -0.310 -0.317 -0.327
PF04422 1.660 1.992 1.792 1.722 1.660 1.660 1.660 1.664
PF04432 1.580 1.904 1.614 1.580 1.557 1.560 1.573 1.576
PF04879 0.226 0.323 0.213 0.170 0.185 0.190 0.213 0.252
PF04898 0.429 -0.182 -0.028 0.337 0.350 0.357 0.361 0.412
PF05088 -0.157 -0.149 -0.153 -0.156 -0.157 -0.157 -0.157 -0.157
PF05369 0.991 1.040 0.991 0.991 0.991 0.991 0.991 0.991
PF05440 3.001 3.032 3.032 2.970 2.955 2.955 2.941 2.955
PF06253 0.587 -0.015 0.591 0.591 0.587 0.587 0.587 0.587
PF06433 0.376 0.024 0.050 0.129 0.327 0.426 0.507 0.446
PF07732 -0.252 -0.175 -0.219 -0.242 -0.244 -0.252 -0.247 -0.240
PF07969 0.101 0.004 0.349 0.281 0.277 0.228 0.222 0.205
PF07992 0.000 -0.093 0.001 0.000 0.000 0.000 0.000 0.000
PF08669 -0.390 -0.238 -0.354 -0.374 -0.383 -0.386 -0.389 -0.389
PF09472 3.032 2.789 2.825 2.982 3.032 3.032 3.032 3.032
PF09505 0.889 0.889 0.889 0.889 0.889 0.889 0.889 0.889
PF09723 -0.079 -0.091 -0.067 -0.088 -0.066 -0.079 -0.079 -0.079
PF10621 1.046 1.061 1.046 1.046 1.046 1.046 1.046 1.046
PF11576 1.298 1.298 1.298 1.298 1.298 1.298 1.298 1.283
PF11844 0.051 -0.002 -0.004 0.005 0.043 0.061 0.058 0.040
PF12176 1.228 1.228 1.228 1.228 1.228 1.228 1.228 1.228
PF12800 0.345 0.536 0.312 0.241 0.240 0.269 0.280 0.289
PF12838 0.122 0.365 0.149 0.120 0.116 0.124 0.122 0.123
PF13187 0.166 0.659 0.247 0.150 0.142 0.149 0.152 0.157
PF13247 0.222 -0.147 0.255 0.245 0.226 0.203 0.185 0.205
PF13360 0.340 0.009 0.242 0.351 0.362 0.358 0.409 0.379
PF13442 -0.295 -0.111 -0.284 -0.304 -0.302 -0.286 -0.293 -0.295
PF13447 0.040 0.068 0.047 0.041 0.039 0.039 0.039 0.038
PF13484 0.160 -0.028 0.236 0.160 0.154 0.155 0.150 0.153
PF13510 -0.212 -0.113 -0.146 -0.044 -0.136 -0.157 -0.127 -0.129
PF13522 0.064 0.150 0.124 0.079 0.073 0.072 0.066 0.064
PF13806 -0.077 -0.106 -0.178 -0.065 -0.071 -0.058 -0.059 -0.074
PF14691 -0.178 -0.087 -0.131 -0.198 -0.145 -0.181 -0.177 -0.164
PF14710 -0.057 0.008 -0.017 -0.015 -0.016 -0.018 0.045 -0.019
PF14711 -0.103 -0.054 -0.084 -0.097 -0.102 -0.102 -0.102 -0.103
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