{"multiple_hits":"None","site_multihit":"Estimate","notified":false,"_id":"5abaac4d149bf22529323b1f","__t":"FEL","ds_variation":1,"status":"completed","mail":"gogarten@uconn.edu","original_extension":"phy","created":"2018-03-27T20:40:45.874Z","msa":[{"datatype":0,"_id":"5abaac4d149bf22529323b20","gencodeid":0,"partitions":1,"sites":610,"sequences":23,"goodtree":0,"nj":"((((((X83276_1:0.02011276195254402,CP004741:0.01791608524629867):0.2263884697805288,FUGC01000:0.2667961804145764):0.06403348844897236,(DS480414:0.001621871675135351,XM_001644:0.004579191539828542):0.3507447250847455):0.1238527421919249,(((XM_459150:0.08853718632842814,XM_015610:0.07541177762703008):0.2113717203797045,XM_020191:0.3534669846194447):0.03217115912137655,(XM_001382:0.324562242645428,(MCFD01000:0.2911302272574292,(KL411544:0.4421282921600795,(XM_016731:0.2952927446612254,KL657804:0.2517886488850811):0.1291451600551143):0.03010836835721864):0.1011228576649538):0.01997035996133068):0.02240062027734324):0.02133051783776285,(XM_455325:0.3929460344903805,AB093505:0.4555593996225037):0.08197001405565485):0.03201749503145174,((XM_001527:0.352693860679514,(XM_002547:0.2680076225820078,BDGI01000:0.2561582837419858):0.01834868813070634):0.08450254626023362,MPUK01000:0.4380656386460979):0.006385541064651057,(XM_022605:0.3028677780772761,((XM_003683:0.2431046100088327,AB093510:0.3277641793945776):0.033474966920606,AB093507:0.2686387759798907):0.02748430198383733):0.07451355931141698)","rawsites":1830,"created":"2018-03-27T20:40:45.875Z","sequence_info":[{"_id":"5abaac4d149bf22529323b21","name":"X83276_1","seqindex":0},{"_id":"5abaac4d149bf22529323b22","name":"CP004741","seqindex":1},{"_id":"5abaac4d149bf22529323b23","name":"XM_455325","seqindex":2},{"_id":"5abaac4d149bf22529323b24","name":"XM_001527","seqindex":3},{"_id":"5abaac4d149bf22529323b25","name":"DS480414","seqindex":4},{"_id":"5abaac4d149bf22529323b26","name":"XM_459150","seqindex":5},{"_id":"5abaac4d149bf22529323b27","name":"XM_001382","seqindex":6},{"_id":"5abaac4d149bf22529323b28","name":"XM_001644","seqindex":7},{"_id":"5abaac4d149bf22529323b29","name":"XM_002547","seqindex":8},{"_id":"5abaac4d149bf22529323b2a","name":"FUGC01000","seqindex":9},{"_id":"5abaac4d149bf22529323b2b","name":"MCFD01000","seqindex":10},{"_id":"5abaac4d149bf22529323b2c","name":"KL411544","seqindex":11},{"_id":"5abaac4d149bf22529323b2d","name":"XM_015610","seqindex":12},{"_id":"5abaac4d149bf22529323b2e","name":"XM_020191","seqindex":13},{"_id":"5abaac4d149bf22529323b2f","name":"XM_016731","seqindex":14},{"_id":"5abaac4d149bf22529323b30","name":"KL657804","seqindex":15},{"_id":"5abaac4d149bf22529323b31","name":"BDGI01000","seqindex":16},{"_id":"5abaac4d149bf22529323b32","name":"XM_022605","seqindex":17},{"_id":"5abaac4d149bf22529323b33","name":"XM_003683","seqindex":18},{"_id":"5abaac4d149bf22529323b34","name":"MPUK01000","seqindex":19},{"_id":"5abaac4d149bf22529323b35","name":"AB093507","seqindex":20},{"_id":"5abaac4d149bf22529323b36","name":"AB093510","seqindex":21},{"_id":"5abaac4d149bf22529323b37","name":"AB093505","seqindex":22}],"partition_info":[{"_id":"5abaac4d149bf22529323b38","span":1830,"endcodon":1829,"startcodon":0,"partition":1}]}],"__v":0,"tagged_nwk_tree":"((((((X83276_1{FG}:0.02011276195254402,CP004741{FG}:0.01791608524629867){FG}:0.2263884697805288,FUGC01000{FG}:0.2667961804145764){FG}:0.06403348844897236,(DS480414{FG}:0.001621871675135351,XM_001644{FG}:0.004579191539828542){FG}:0.3507447250847455){FG}:0.1238527421919249,(((XM_459150{FG}:0.08853718632842814,XM_015610{FG}:0.07541177762703008){FG}:0.2113717203797045,XM_020191{FG}:0.3534669846194447){FG}:0.03217115912137655,(XM_001382{FG}:0.324562242645428,(MCFD01000{FG}:0.2911302272574292,(KL411544{FG}:0.4421282921600795,(XM_016731{FG}:0.2952927446612254,KL657804{FG}:0.2517886488850811){FG}:0.1291451600551143){FG}:0.03010836835721864){FG}:0.1011228576649538){FG}:0.01997035996133068){FG}:0.02240062027734324){FG}:0.02133051783776285,(XM_455325{FG}:0.3929460344903805,AB093505{FG}:0.4555593996225037){FG}:0.08197001405565485){FG}:0.03201749503145174,((XM_001527{FG}:0.352693860679514,(XM_002547{FG}:0.2680076225820078,BDGI01000{FG}:0.2561582837419858){FG}:0.01834868813070634){FG}:0.08450254626023362,MPUK01000{FG}:0.4380656386460979){FG}:0.006385541064651057,(XM_022605{FG}:0.3028677780772761,((XM_003683{FG}:0.2431046100088327,AB093510{FG}:0.3277641793945776){FG}:0.033474966920606,AB093507{FG}:0.2686387759798907){FG}:0.02748430198383733){FG}:0.07451355931141698)","creation_time":"2018-03-27T20:41:02.000Z","last_status_msg":"\nAnalysis Description\n--------------------\nFEL (Fixed Effects Likelihood) estimates site-wise synonymous (α)\nand non-synonymous (β) rates, and uses a likelihood ratio test to\ndetermine if beta &neq; alpha at a site. The estimates aggregate\ninformation over all branches, so the signal is derived from pervasive\ndiversification or conservation. A subset of branches can be selected\nfor testing as well, in which case an additional (nuisance) parameter\nwill be inferred -- the non-synonymous rate on branches NOT selected for\ntesting. Multiple partitions within a NEXUS file are also supported for\nrecombination - aware analysis. \n\n- __Requirements__: in-frame codon alignment and a phylogenetic tree\n\n- __Citation__: Not So Different After All: A Comparison of Methods for Detecting Amino\nAcid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222\n\n- __Written by__: Sergei L Kosakovsky Pond and Simon DW Frost\n\n- __Contact Information__: spond@temple.edu\n\n- __Analysis Version__: 2.00\n\n\n\n####Choose Genetic Code\n\n1. [**Universal**] Universal code. (Genebank transl_table=1).\n2. [**Vertebrate mtDNA**] Vertebrate mitochondrial DNA code. (Genebank transl_table=2).\n3. [**Yeast mtDNA**] Yeast mitochondrial DNA code. (Genebank transl_table=3).\n4. [**Mold/Protozoan mtDNA**] Mold, Protozoan and Coelenterate mitochondrial DNA and the Mycloplasma/Spiroplasma code. (Genebank transl_table=4).\n5. [**Invertebrate mtDNA**] Invertebrate mitochondrial DNA code. (Genebank transl_table=5).\n6. [**Ciliate Nuclear**] Ciliate, Dasycladacean and Hexamita Nuclear code. (Genebank transl_table=6).\n7. [**Echinoderm mtDNA**] Echinoderm mitochondrial DNA code. (Genebank transl_table=9).\n8. [**Euplotid Nuclear**] Euplotid Nuclear code. (Genebank transl_table=10).\n9. [**Alt. Yeast Nuclear**] Alternative Yeast Nuclear code. (Genebank transl_table=12).\n10. [**Ascidian mtDNA**] Ascidian mitochondrial DNA code. (Genebank transl_table=13).\n11. [**Flatworm mtDNA**] Flatworm mitochondrial DNA code. (Genebank transl_table=14).\n12. [**Blepharisma Nuclear**] Blepharisma Nuclear code. (Genebank transl_table=15).\n13. [**Chlorophycean mtDNA**] Chlorophycean Mitochondrial Code (transl_table=16).\n14. [**Trematode mtDNA**] Trematode Mitochondrial Code (transl_table=21).\n15. [**Scenedesmus obliquus mtDNA**] Scenedesmus obliquus mitochondrial Code (transl_table=22).\n16. [**Thraustochytrium mtDNA**] Thraustochytrium Mitochondrial Code (transl_table=23).\n17. [**Pterobranchia mtDNA**] Pterobranchia Mitochondrial Code (transl_table=24).\n18. [**SR1 and Gracilibacteria**] Candidate Division SR1 and Gracilibacteria Code (transl_table=25).\n19. [**Pachysolen Nuclear**] Pachysolen tannophilus Nuclear Code (transl_table=26).\n\n>Please choose an option (or press q to cancel selection):\n\n>Select a coding sequence alignment file (`/home/datamonkey/datamonkey-js-test/app/fel/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) \n\n>Please select a tree file for the data: (`/home/datamonkey/datamonkey-js-test/app/fel/../../.hyphy/res//TemplateBatchFiles/SelectionAnalyses/`) \n>Loaded a multiple sequence alignment with **23** sequences, **610** codons, and **1** partitions from `/home/datamonkey/datamonkey-js-test/app/fel/output/5abaac4d149bf22529323b1f`\n\n\n####Choose the set of branches to test for selection\n\n1. [**All**] Include all branches in the analysis\n2. [**Internal**] Include all internal branches in the analysis\n3. [**Leaves**] Include all leaf branches in the analysis\n4. [**FG**] Set FG with 43 branches\n\n>Please choose an option (or press q to cancel selection):\n\n####Use synonymous rate variation? Strongly recommended YES for selection inference.\n\n1. [**Yes**] [Recommended] Consider synonymous rate variation (dS varies across sites).\n2. [**No**] Ignore synonymous rate variation (dS := 1 at each site).\n\n>Please choose an option (or press q to cancel selection):Yes\n\n>Select the p-value threshold to use when testing for selection (permissible range = [0,1], default value = 0.1): \n\n### Branches to include in the FEL analysis\nSelected 43 branches to include in FEL calculations: `X83276_1, CP004741, Node5, FUGC01000, Node4, DS480414, XM_001644, Node9, Node3, XM_459150, XM_015610, Node14, XM_020191, Node13, XM_001382, MCFD01000, KL411544, XM_016731, KL657804, Node24, Node22, Node20, Node18, Node12, Node2, XM_455325, AB093505, Node27, Node1, XM_001527, XM_002547, BDGI01000, Node33, Node31, MPUK01000, Node30, XM_022605, XM_003683, AB093510, Node40, AB093507, Node39, Node37`\n\n\n### Obtaining branch lengths and nucleotide substitution biases under the nucleotide GTR model\n* Log(L) = -31399.52, AIC-c = 62901.16 (51 estimated parameters)\n\n### Obtaining the global omega estimate based on relative GTR branch lengths and nucleotide substitution biases\n* Log(L) = -30184.64, AIC-c = 60485.78 (58 estimated parameters)\n* non-synonymous/synonymous rate ratio for *test* = 0.2636\n\n### Improving branch lengths, nucleotide substitution biases, and global dN/dS ratios under a full codon model\n* Log(L) = -30041.71\n* non-synonymous/synonymous rate ratio for *test* = 0.1982\n\n### For partition 1 these sites are significant at p <=0.1\n\n| Codon | Partition | alpha | beta | LRT |Selection detected?|\n|:--------------:|:--------------:|:--------------:|:--------------:|:--------------:|:-----------------:|\n| 1 | 1 | 0.549 | 0.000 | 16.931 | Neg. p = 0.0000 |\n| 2 | 1 | 7.029 | 0.000 | 34.063 | Neg. p = 0.0000 |\n| 3 | 1 | 4.627 | 0.049 | 10.473 | Neg. p = 0.0012 |\n| 4 | 1 | 2.365 | 0.036 | 16.015 | Neg. p = 0.0001 |\n| 5 | 1 | 0.338 | 0.015 | 12.606 | Neg. p = 0.0004 |\n| 6 | 1 | 0.560 | 0.000 | 27.731 | Neg. p = 0.0000 |\n| 7 | 1 | 3.442 | 0.179 | 8.355 | Neg. p = 0.0038 |\n| 8 | 1 | 0.397 | 0.000 | 20.891 | Neg. p = 0.0000 |\n| 9 | 1 | 1.515 | 0.097 | 10.900 | Neg. p = 0.0010 |\n| 11 | 1 | 0.356 | 0.061 | 7.462 | Neg. p = 0.0063 |\n| 12 | 1 | 7.043 | 0.037 | 17.571 | Neg. p = 0.0000 |\n| 13 | 1 | 0.313 | 0.031 | 8.223 | Neg. p = 0.0041 |\n| 14 | 1 | 4.181 | 0.291 | 6.105 | Neg. p = 0.0135 |\n| 15 | 1 | 1.081 | 0.130 | 9.146 | Neg. p = 0.0025 |\n| 16 | 1 | 1.491 | 0.048 | 17.510 | Neg. p = 0.0000 |\n| 17 | 1 | 4.550 | 0.547 | 3.909 | Neg. p = 0.0480 |\n| 18 | 1 | 0.440 | 0.059 | 8.442 | Neg. p = 0.0037 |\n| 19 | 1 | 31.750 | 0.012 | 35.281 | Neg. p = 0.0000 |\n| 21 | 1 | 0.216 | 0.060 | 2.755 | Neg. p = 0.0969 |\n| 22 | 1 | 1.474 | 0.266 | 3.595 | Neg. p = 0.0580 |\n| 23 | 1 | 0.799 | 0.230 | 3.344 | Neg. p = 0.0675 |\n| 24 | 1 | 0.202 | 0.032 | 4.113 | Neg. p = 0.0426 |\n| 25 | 1 | 0.832 | 0.094 | 5.341 | Neg. p = 0.0208 |\n| 27 | 1 | 0.306 | 0.000 | 17.319 | Neg. p = 0.0000 |\n| 28 | 1 | 2.437 | 0.033 | 9.334 | Neg. p = 0.0022 |\n| 29 | 1 | 0.196 | 0.000 | 11.380 | Neg. p = 0.0007 |\n| 30 | 1 | 0.567 | 0.076 | 5.413 | Neg. p = 0.0200 |\n| 31 | 1 | 0.544 | 0.000 | 18.291 | Neg. p = 0.0000 |\n| 32 | 1 | 0.218 | 0.000 | 12.167 | Neg. p = 0.0005 |\n| 34 | 1 | 0.343 | 0.053 | 8.840 | Neg. p = 0.0029 |\n| 35 | 1 | 0.516 | 0.000 | 24.071 | Neg. p = 0.0000 |\n| 36 | 1 | 1.685 | 0.330 | 3.644 | Neg. p = 0.0563 |\n| 37 | 1 | 0.605 | 0.000 | 22.578 | Neg. p = 0.0000 |\n| 40 | 1 | 3.323 | 0.000 | 52.969 | Neg. p = 0.0000 |\n| 41 | 1 | 0.160 | 0.000 | 12.419 | Neg. p = 0.0004 |\n| 42 | 1 | 0.890 | 0.026 | 22.353 | Neg. p = 0.0000 |\n| 43 | 1 | 0.451 | 0.000 | 21.521 | Neg. p = 0.0000 |\n| 45 | 1 | 3.205 | 0.132 | 6.035 | Neg. p = 0.0140 |\n| 46 | 1 | 1.078 | 0.101 | 14.568 | Neg. p = 0.0001 |\n| 48 | 1 | 0.214 | 0.000 | 9.648 | Neg. p = 0.0019 |\n| 49 | 1 | 36.292 | 0.205 | 18.172 | Neg. p = 0.0000 |\n| 50 | 1 | 0.534 | 0.036 | 13.572 | Neg. p = 0.0002 |\n| 52 | 1 | 1.179 | 0.174 | 7.218 | Neg. p = 0.0072 |\n| 53 | 1 | 1.071 | 0.227 | 4.025 | Neg. p = 0.0448 |\n| 54 | 1 | 0.826 | 0.281 | 3.240 | Neg. p = 0.0719 |\n| 55 | 1 | 32.386 | 0.205 | 9.463 | Neg. p = 0.0021 |\n| 56 | 1 | 1.012 | 0.184 | 6.818 | Neg. p = 0.0090 |\n| 59 | 1 | 20.382 | 0.363 | 6.010 | Neg. p = 0.0142 |\n| 60 | 1 | 2.398 | 0.232 | 7.319 | Neg. p = 0.0068 |\n| 68 | 1 | 1.556 | 0.000 | 3.648 | Neg. p = 0.0561 |\n| 70 | 1 | 1.000 | 0.213 | 5.562 | Neg. p = 0.0184 |\n| 72 | 1 | 1.004 | 0.216 | 3.756 | Neg. p = 0.0526 |\n| 73 | 1 | 1.602 | 0.311 | 4.791 | Neg. p = 0.0286 |\n| 74 | 1 | 0.711 | 0.063 | 12.107 | Neg. p = 0.0005 |\n| 75 | 1 | 0.858 | 0.183 | 4.811 | Neg. p = 0.0283 |\n| 76 | 1 | 0.464 | 0.032 | 8.716 | Neg. p = 0.0032 |\n| 77 | 1 | 0.557 | 0.026 | 14.260 | Neg. p = 0.0002 |\n| 78 | 1 | 0.956 | 0.117 | 11.165 | Neg. p = 0.0008 |\n| 79 | 1 | 15.342 | 0.136 | 20.224 | Neg. p = 0.0000 |\n| 80 | 1 | 7.049 | 0.000 | 39.530 | Neg. p = 0.0000 |\n| 81 | 1 | 0.505 | 0.169 | 2.784 | Neg. p = 0.0952 |\n| 82 | 1 | 1.354 | 0.018 | 27.681 | Neg. p = 0.0000 |\n| 83 | 1 | 0.359 | 0.036 | 8.775 | Neg. p = 0.0031 |\n| 84 | 1 | 1.062 | 0.076 | 13.396 | Neg. p = 0.0003 |\n| 86 | 1 | 0.390 | 0.000 | 20.606 | Neg. p = 0.0000 |\n| 87 | 1 | 0.450 | 0.150 | 3.279 | Neg. p = 0.0702 |\n| 88 | 1 | 3.062 | 0.012 | 20.443 | Neg. p = 0.0000 |\n| 89 | 1 | 21.917 | 0.243 | 10.991 | Neg. p = 0.0009 |\n| 92 | 1 | 5.893 | 0.307 | 3.851 | Neg. p = 0.0497 |\n| 93 | 1 | 4.462 | 0.136 | 6.392 | Neg. p = 0.0115 |\n| 94 | 1 | 1.845 | 0.188 | 6.665 | Neg. p = 0.0098 |\n| 95 | 1 | 0.495 | 0.050 | 8.663 | Neg. p = 0.0032 |\n| 100 | 1 | 2.407 | 0.104 | 13.867 | Neg. p = 0.0002 |\n| 102 | 1 | 0.822 | 0.175 | 4.549 | Neg. p = 0.0329 |\n| 103 | 1 | 0.517 | 0.190 | 2.991 | Neg. p = 0.0837 |\n| 104 | 1 | 0.789 | 0.182 | 4.532 | Neg. p = 0.0333 |\n| 105 | 1 | 0.422 | 0.018 | 13.221 | Neg. p = 0.0003 |\n| 106 | 1 | 0.678 | 0.250 | 3.379 | Neg. p = 0.0660 |\n| 107 | 1 | 1.924 | 0.196 | 10.306 | Neg. p = 0.0013 |\n| 108 | 1 | 0.839 | 0.099 | 8.979 | Neg. p = 0.0027 |\n| 109 | 1 | 4.887 | 0.302 | 7.257 | Neg. p = 0.0071 |\n| 110 | 1 | 0.838 | 0.209 | 2.885 | Neg. p = 0.0894 |\n| 111 | 1 | 19.225 | 0.305 | 10.722 | Neg. p = 0.0011 |\n| 112 | 1 | 5.680 | 0.295 | 4.598 | Neg. p = 0.0320 |\n| 113 | 1 | 1.794 | 0.252 | 6.781 | Neg. p = 0.0092 |\n| 114 | 1 | 26.885 | 0.381 | 6.688 | Neg. p = 0.0097 |\n| 116 | 1 | 2.277 | 0.323 | 4.727 | Neg. p = 0.0297 |\n| 117 | 1 | 0.987 | 0.154 | 3.985 | Neg. p = 0.0459 |\n| 118 | 1 | 3.483 | 0.181 | 8.958 | Neg. p = 0.0028 |\n| 124 | 1 | 0.679 | 0.039 | 10.832 | Neg. p = 0.0010 |\n| 127 | 1 | 1.315 | 0.222 | 5.772 | Neg. p = 0.0163 |\n| 128 | 1 | 0.785 | 0.212 | 2.881 | Neg. p = 0.0896 |\n| 129 | 1 | 0.944 | 0.075 | 16.044 | Neg. p = 0.0001 |\n| 130 | 1 | 0.723 | 0.078 | 10.647 | Neg. p = 0.0011 |\n| 131 | 1 | 4.743 | 0.280 | 7.545 | Neg. p = 0.0060 |\n| 133 | 1 | 1.047 | 0.103 | 12.784 | Neg. p = 0.0003 |\n| 134 | 1 | 5.108 | 0.074 | 21.333 | Neg. p = 0.0000 |\n| 135 | 1 | 3.403 | 0.236 | 4.584 | Neg. p = 0.0323 |\n| 136 | 1 | 30.672 | 0.085 | 28.597 | Neg. p = 0.0000 |\n| 138 | 1 | 3.571 | 0.107 | 12.195 | Neg. p = 0.0005 |\n| 141 | 1 | 16.985 | 0.137 | 17.468 | Neg. p = 0.0000 |\n| 142 | 1 | 2.042 | 0.043 | 8.690 | Neg. p = 0.0032 |\n| 143 | 1 | 0.496 | 0.019 | 12.539 | Neg. p = 0.0004 |\n| 145 | 1 | 7.036 | 0.259 | 6.155 | Neg. p = 0.0131 |\n| 147 | 1 | 0.567 | 0.052 | 10.249 | Neg. p = 0.0014 |\n| 150 | 1 | 19.136 | 0.221 | 22.594 | Neg. p = 0.0000 |\n| 151 | 1 | 2.975 | 0.030 | 23.190 | Neg. p = 0.0000 |\n| 152 | 1 | 2.632 | 0.380 | 6.614 | Neg. p = 0.0101 |\n| 153 | 1 | 4.423 | 0.467 | 4.715 | Neg. p = 0.0299 |\n| 154 | 1 | 1.460 | 0.049 | 16.204 | Neg. p = 0.0001 |\n| 155 | 1 | 0.796 | 0.210 | 3.942 | Neg. p = 0.0471 |\n| 157 | 1 | 2.133 | 0.315 | 7.335 | Neg. p = 0.0068 |\n| 159 | 1 | 2125.302 | 0.102 | 2.731 | Neg. p = 0.0984 |\n| 164 | 1 | 0.214 | 0.046 | 3.015 | Neg. p = 0.0825 |\n| 165 | 1 | 1.556 | 0.182 | 6.650 | Neg. p = 0.0099 |\n| 167 | 1 | 0.310 | 0.089 | 3.074 | Neg. p = 0.0796 |\n| 168 | 1 | 1.185 | 0.118 | 7.723 | Neg. p = 0.0055 |\n| 169 | 1 | 1.658 | 0.038 | 16.829 | Neg. p = 0.0000 |\n| 170 | 1 | 0.529 | 0.045 | 13.385 | Neg. p = 0.0003 |\n| 171 | 1 | 7.410 | 0.116 | 22.273 | Neg. p = 0.0000 |\n| 172 | 1 | 0.726 | 0.026 | 14.576 | Neg. p = 0.0001 |\n| 173 | 1 | 1.087 | 0.176 | 9.404 | Neg. p = 0.0022 |\n| 187 | 1 | 1.822 | 0.459 | 3.061 | Neg. p = 0.0802 |\n| 188 | 1 | 0.930 | 0.073 | 15.489 | Neg. p = 0.0001 |\n| 189 | 1 | 1.157 | 0.293 | 4.211 | Neg. p = 0.0402 |\n| 191 | 1 | 1.733 | 0.223 | 9.362 | Neg. p = 0.0022 |\n| 192 | 1 | 0.531 | 0.055 | 10.952 | Neg. p = 0.0009 |\n| 193 | 1 | 0.445 | 0.013 | 14.599 | Neg. p = 0.0001 |\n| 194 | 1 | 11.498 | 0.163 | 14.539 | Neg. p = 0.0001 |\n| 195 | 1 | 0.801 | 0.123 | 10.483 | Neg. p = 0.0012 |\n| 196 | 1 | 0.636 | 0.049 | 15.553 | Neg. p = 0.0001 |\n| 197 | 1 | 6.978 | 0.149 | 10.634 | Neg. p = 0.0011 |\n| 198 | 1 | 0.477 | 0.000 | 17.863 | Neg. p = 0.0000 |\n| 199 | 1 | 1.550 | 0.258 | 3.784 | Neg. p = 0.0517 |\n| 200 | 1 | 0.790 | 0.162 | 3.934 | Neg. p = 0.0473 |\n| 201 | 1 | 0.845 | 0.119 | 7.770 | Neg. p = 0.0053 |\n| 202 | 1 | 0.224 | 0.000 | 16.187 | Neg. p = 0.0001 |\n| 203 | 1 | 0.839 | 0.061 | 13.668 | Neg. p = 0.0002 |\n| 204 | 1 | 6.162 | 0.073 | 31.608 | Neg. p = 0.0000 |\n| 206 | 1 | 0.901 | 0.056 | 11.565 | Neg. p = 0.0007 |\n| 210 | 1 | 1.365 | 0.089 | 14.895 | Neg. p = 0.0001 |\n| 211 | 1 | 1.866 | 0.258 | 6.273 | Neg. p = 0.0123 |\n| 214 | 1 | 1.926 | 0.101 | 19.311 | Neg. p = 0.0000 |\n| 219 | 1 | 2.276 | 0.218 | 7.400 | Neg. p = 0.0065 |\n| 221 | 1 | 4.666 | 0.400 | 4.901 | Neg. p = 0.0268 |\n| 225 | 1 | 0.345 | 0.093 | 4.120 | Neg. p = 0.0424 |\n| 226 | 1 | 0.467 | 0.165 | 3.594 | Neg. p = 0.0580 |\n| 229 | 1 | 4.973 | 0.157 | 15.476 | Neg. p = 0.0001 |\n| 230 | 1 | 0.534 | 0.046 | 13.205 | Neg. p = 0.0003 |\n| 231 | 1 | 1.530 | 0.036 | 17.387 | Neg. p = 0.0000 |\n| 232 | 1 | 2.652 | 0.037 | 30.714 | Neg. p = 0.0000 |\n| 233 | 1 | 1.307 | 0.070 | 18.503 | Neg. p = 0.0000 |\n| 234 | 1 | 0.092 | 0.000 | 5.620 | Neg. p = 0.0178 |\n| 235 | 1 | 0.652 | 0.219 | 2.731 | Neg. p = 0.0984 |\n| 236 | 1 | 7.334 | 0.075 | 4.411 | Neg. p = 0.0357 |\n| 238 | 1 | 0.218 | 0.046 | 3.841 | Neg. p = 0.0500 |\n| 242 | 1 | 1.841 | 0.260 | 7.782 | Neg. p = 0.0053 |\n| 243 | 1 | 0.920 | 0.103 | 12.479 | Neg. p = 0.0004 |\n| 245 | 1 | 3.562 | 0.247 | 10.706 | Neg. p = 0.0011 |\n| 246 | 1 | 1.784 | 0.276 | 5.988 | Neg. p = 0.0144 |\n| 247 | 1 | 1.551 | 0.306 | 3.999 | Neg. p = 0.0455 |\n| 250 | 1 | 4.000 | 0.182 | 10.606 | Neg. p = 0.0011 |\n| 253 | 1 | 1.094 | 0.163 | 6.051 | Neg. p = 0.0139 |\n| 256 | 1 | 6.273 | 0.084 | 19.727 | Neg. p = 0.0000 |\n| 259 | 1 | 2.241 | 0.221 | 8.215 | Neg. p = 0.0042 |\n| 260 | 1 | 0.626 | 0.192 | 3.050 | Neg. p = 0.0808 |\n| 262 | 1 | 9.200 | 0.303 | 7.942 | Neg. p = 0.0048 |\n| 263 | 1 | 0.980 | 0.131 | 6.641 | Neg. p = 0.0100 |\n| 264 | 1 | 4.812 | 0.136 | 12.091 | Neg. p = 0.0005 |\n| 267 | 1 | 1.786 | 0.413 | 2.905 | Neg. p = 0.0883 |\n| 269 | 1 | 2.895 | 0.398 | 4.134 | Neg. p = 0.0420 |\n| 271 | 1 | 5.986 | 0.137 | 20.571 | Neg. p = 0.0000 |\n| 273 | 1 | 3.238 | 0.080 | 27.425 | Neg. p = 0.0000 |\n| 277 | 1 | 2.018 | 0.290 | 4.472 | Neg. p = 0.0345 |\n| 278 | 1 | 2.346 | 0.249 | 6.301 | Neg. p = 0.0121 |\n| 302 | 1 | 17.908 | 0.335 | 10.331 | Neg. p = 0.0013 |\n| 303 | 1 | 3.815 | 0.430 | 4.000 | Neg. p = 0.0455 |\n| 304 | 1 | 2.346 | 0.323 | 4.711 | Neg. p = 0.0300 |\n| 306 | 1 | 5.856 | 0.338 | 3.032 | Neg. p = 0.0816 |\n| 334 | 1 | 2405.406 | 0.382 | 3.561 | Neg. p = 0.0591 |\n| 336 | 1 | 6.040 | 0.250 | 4.510 | Neg. p = 0.0337 |\n| 337 | 1 | 2251.154 | 0.187 | 4.034 | Neg. p = 0.0446 |\n| 361 | 1 | 2408.304 | 0.342 | 3.289 | Neg. p = 0.0698 |\n| 362 | 1 | 0.000 | 1.560 | 3.127 | Pos. p = 0.0770 |\n| 379 | 1 | 131.833 | 0.000 | 5.664 | Neg. p = 0.0173 |\n| 383 | 1 | 6.464 | 0.000 | 3.246 | Neg. p = 0.0716 |\n| 385 | 1 | 0.389 | 0.000 | 3.158 | Neg. p = 0.0756 |\n| 386 | 1 | 8.312 | 0.382 | 2.839 | Neg. p = 0.0920 |\n| 390 | 1 | 2.895 | 0.399 | 5.061 | Neg. p = 0.0245 |\n| 391 | 1 | 2.457 | 0.398 | 3.633 | Neg. p = 0.0567 |\n| 392 | 1 | 6.831 | 0.444 | 5.625 | Neg. p = 0.0177 |\n| 393 | 1 | 2.121 | 0.126 | 12.884 | Neg. p = 0.0003 |\n| 394 | 1 | 1.615 | 0.401 | 3.002 | Neg. p = 0.0832 |\n| 395 | 1 | 34.141 | 0.471 | 5.599 | Neg. p = 0.0180 |\n| 396 | 1 | 1.035 | 0.071 | 10.794 | Neg. p = 0.0010 |\n| 397 | 1 | 5.717 | 0.360 | 6.948 | Neg. p = 0.0084 |\n| 399 | 1 | 4.422 | 0.140 | 8.411 | Neg. p = 0.0037 |\n| 405 | 1 | 8.322 | 0.190 | 11.314 | Neg. p = 0.0008 |\n| 406 | 1 | 0.559 | 0.068 | 10.420 | Neg. p = 0.0012 |\n| 408 | 1 | 1.020 | 0.215 | 2.757 | Neg. p = 0.0969 |\n| 409 | 1 | 8.561 | 0.348 | 5.742 | Neg. p = 0.0166 |\n| 425 | 1 | 0.670 | 0.050 | 12.296 | Neg. p = 0.0005 |\n| 428 | 1 | 0.236 | 0.012 | 10.293 | Neg. p = 0.0013 |\n| 431 | 1 | 1.390 | 0.099 | 12.446 | Neg. p = 0.0004 |\n| 432 | 1 | 0.979 | 0.254 | 4.764 | Neg. p = 0.0291 |\n| 434 | 1 | 0.230 | 0.038 | 2.784 | Neg. p = 0.0952 |\n| 435 | 1 | 2.100 | 0.311 | 4.913 | Neg. p = 0.0266 |\n| 436 | 1 | 0.809 | 0.097 | 8.810 | Neg. p = 0.0030 |\n| 437 | 1 | 5.485 | 0.321 | 5.193 | Neg. p = 0.0227 |\n| 438 | 1 | 0.511 | 0.075 | 7.537 | Neg. p = 0.0060 |\n| 439 | 1 | 0.346 | 0.000 | 17.839 | Neg. p = 0.0000 |\n| 440 | 1 | 0.471 | 0.000 | 17.864 | Neg. p = 0.0000 |\n| 441 | 1 | 5.131 | 0.359 | 6.106 | Neg. p = 0.0135 |\n| 442 | 1 | 0.501 | 0.029 | 11.805 | Neg. p = 0.0006 |\n| 443 | 1 | 2.418 | 0.136 | 12.035 | Neg. p = 0.0005 |\n| 444 | 1 | 0.443 | 0.029 | 13.282 | Neg. p = 0.0003 |\n| 445 | 1 | 0.162 | 0.000 | 9.115 | Neg. p = 0.0025 |\n| 446 | 1 | 1.330 | 0.056 | 23.341 | Neg. p = 0.0000 |\n| 447 | 1 | 0.460 | 0.112 | 4.832 | Neg. p = 0.0279 |\n| 448 | 1 | 1.951 | 0.000 | 36.287 | Neg. p = 0.0000 |\n| 449 | 1 | 0.898 | 0.100 | 9.725 | Neg. p = 0.0018 |\n| 450 | 1 | 4.522 | 0.159 | 10.746 | Neg. p = 0.0010 |\n| 451 | 1 | 4.150 | 0.064 | 18.417 | Neg. p = 0.0000 |\n| 453 | 1 | 0.712 | 0.087 | 7.437 | Neg. p = 0.0064 |\n| 456 | 1 | 0.961 | 0.237 | 3.627 | Neg. p = 0.0568 |\n| 477 | 1 | 4.189 | 0.484 | 2.840 | Neg. p = 0.0919 |\n| 478 | 1 | 15.851 | 0.158 | 14.824 | Neg. p = 0.0001 |\n| 479 | 1 | 1.494 | 0.175 | 7.611 | Neg. p = 0.0058 |\n| 480 | 1 | 0.576 | 0.149 | 3.985 | Neg. p = 0.0459 |\n| 482 | 1 | 3.237 | 0.084 | 17.361 | Neg. p = 0.0000 |\n| 485 | 1 | 2.936 | 0.263 | 6.602 | Neg. p = 0.0102 |\n| 487 | 1 | 0.485 | 0.162 | 3.698 | Neg. p = 0.0545 |\n| 488 | 1 | 2.513 | 0.346 | 5.280 | Neg. p = 0.0216 |\n| 489 | 1 | 24.261 | 0.188 | 9.275 | Neg. p = 0.0023 |\n| 490 | 1 | 21.818 | 0.064 | 22.183 | Neg. p = 0.0000 |\n| 491 | 1 | 2.609 | 0.185 | 9.747 | Neg. p = 0.0018 |\n| 492 | 1 | 0.554 | 0.094 | 7.218 | Neg. p = 0.0072 |\n| 493 | 1 | 0.775 | 0.228 | 3.983 | Neg. p = 0.0460 |\n| 494 | 1 | 3.662 | 0.178 | 8.237 | Neg. p = 0.0041 |\n| 495 | 1 | 0.522 | 0.080 | 9.244 | Neg. p = 0.0024 |\n| 496 | 1 | 0.183 | 0.013 | 7.399 | Neg. p = 0.0065 |\n| 497 | 1 | 4.655 | 0.000 | 32.397 | Neg. p = 0.0000 |\n| 498 | 1 | 3.114 | 0.000 | 53.622 | Neg. p = 0.0000 |\n| 499 | 1 | 0.180 | 0.000 | 9.864 | Neg. p = 0.0017 |\n| 500 | 1 | 5.109 | 0.064 | 20.116 | Neg. p = 0.0000 |\n| 501 | 1 | 11.926 | 0.221 | 12.622 | Neg. p = 0.0004 |\n| 503 | 1 | 0.502 | 0.160 | 3.193 | Neg. p = 0.0739 |\n| 504 | 1 | 14.856 | 0.174 | 7.141 | Neg. p = 0.0075 |\n| 505 | 1 | 1.716 | 0.233 | 7.716 | Neg. p = 0.0055 |\n| 510 | 1 | 2.385 | 0.063 | 7.952 | Neg. p = 0.0048 |\n| 511 | 1 | 6.340 | 0.262 | 3.727 | Neg. p = 0.0535 |\n| 512 | 1 | 4.320 | 0.381 | 3.774 | Neg. p = 0.0521 |\n| 515 | 1 | 2.114 | 0.154 | 8.110 | Neg. p = 0.0044 |\n| 518 | 1 | 0.450 | 0.127 | 3.141 | Neg. p = 0.0764 |\n| 520 | 1 | 1.092 | 0.229 | 3.562 | Neg. p = 0.0591 |\n| 521 | 1 | 1.365 | 0.123 | 7.717 | Neg. p = 0.0055 |\n| 522 | 1 | 9.685 | 0.401 | 3.294 | Neg. p = 0.0695 |\n| 523 | 1 | 18.401 | 0.464 | 5.704 | Neg. p = 0.0169 |\n| 533 | 1 | 0.656 | 0.070 | 9.426 | Neg. p = 0.0021 |\n| 535 | 1 | 1.838 | 0.179 | 9.848 | Neg. p = 0.0017 |\n| 537 | 1 | 0.887 | 0.142 | 5.472 | Neg. p = 0.0193 |\n| 539 | 1 | 0.305 | 0.098 | 2.834 | Neg. p = 0.0923 |\n| 542 | 1 | 0.000 | 0.639 | 2.956 | Pos. p = 0.0856 |\n| 545 | 1 | 0.443 | 0.127 | 3.966 | Neg. p = 0.0464 |\n| 546 | 1 | 1.686 | 0.060 | 21.788 | Neg. p = 0.0000 |\n| 548 | 1 | 1.017 | 0.223 | 6.081 | Neg. p = 0.0137 |\n| 550 | 1 | 0.986 | 0.077 | 15.340 | Neg. p = 0.0001 |\n| 551 | 1 | 0.776 | 0.181 | 3.108 | Neg. p = 0.0779 |\n| 552 | 1 | 8.021 | 0.198 | 11.308 | Neg. p = 0.0008 |\n| 553 | 1 | 0.464 | 0.048 | 7.219 | Neg. p = 0.0072 |\n| 557 | 1 | 1.097 | 0.160 | 8.542 | Neg. p = 0.0035 |\n| 558 | 1 | 1.512 | 0.129 | 7.496 | Neg. p = 0.0062 |\n| 560 | 1 | 1.014 | 0.255 | 3.263 | Neg. p = 0.0709 |\n| 565 | 1 | 1.688 | 0.398 | 4.013 | Neg. p = 0.0452 |\n| 568 | 1 | 0.514 | 0.103 | 4.910 | Neg. p = 0.0267 |\n| 569 | 1 | 1.367 | 0.296 | 2.707 | Neg. p = 0.0999 |\n| 570 | 1 | 0.220 | 0.013 | 6.733 | Neg. p = 0.0095 |\n| 571 | 1 | 4.663 | 0.193 | 10.617 | Neg. p = 0.0011 |\n| 572 | 1 | 0.787 | 0.257 | 2.951 | Neg. p = 0.0858 |\n| 573 | 1 | 22.730 | 0.159 | 11.390 | Neg. p = 0.0007 |\n| 574 | 1 | 7.662 | 0.185 | 12.628 | Neg. p = 0.0004 |\n| 576 | 1 | 0.738 | 0.184 | 4.824 | Neg. p = 0.0281 |\n| 577 | 1 | 5.729 | 0.000 | 33.874 | Neg. p = 0.0000 |\n| 579 | 1 | 2.988 | 0.144 | 14.926 | Neg. p = 0.0001 |\n| 581 | 1 | 0.544 | 0.110 | 4.182 | Neg. p = 0.0409 |\n| 582 | 1 | 17.208 | 0.236 | 19.186 | Neg. p = 0.0000 |\n| 584 | 1 | 6.006 | 0.196 | 11.825 | Neg. p = 0.0006 |\n| 585 | 1 | 0.842 | 0.093 | 9.878 | Neg. p = 0.0017 |\n| 586 | 1 | 1.420 | 0.193 | 6.324 | Neg. p = 0.0119 |\n| 587 | 1 | 0.459 | 0.017 | 12.346 | Neg. p = 0.0004 |\n| 588 | 1 | 30.419 | 0.035 | 29.933 | Neg. p = 0.0000 |\n| 589 | 1 | 0.146 | 0.000 | 8.598 | Neg. p = 0.0034 |\n| 591 | 1 | 0.547 | 0.000 | 27.804 | Neg. p = 0.0000 |\n| 592 | 1 | 2.822 | 0.017 | 40.295 | Neg. p = 0.0000 |\n| 593 | 1 | 0.653 | 0.173 | 5.414 | Neg. p = 0.0200 |\n| 594 | 1 | 5.532 | 0.110 | 11.143 | Neg. p = 0.0008 |\n| 595 | 1 | 2.452 | 0.327 | 2.802 | Neg. p = 0.0942 |\n| 596 | 1 | 0.730 | 0.088 | 10.279 | Neg. p = 0.0013 |\n| 597 | 1 | 2.399 | 0.000 | 38.850 | Neg. p = 0.0000 |\n| 598 | 1 | 7.917 | 0.022 | 33.062 | Neg. p = 0.0000 |\n| 599 | 1 | 1.232 | 0.091 | 13.233 | Neg. p = 0.0003 |\n| 600 | 1 | 0.707 | 0.015 | 16.108 | Neg. p = 0.0001 |\n| 601 | 1 | 0.969 | 0.056 | 18.650 | Neg. p = 0.0000 |\n| 602 | 1 | 2.108 | 0.000 | 41.063 | Neg. p = 0.0000 |\n| 603 | 1 | 0.604 | 0.102 | 8.794 | Neg. p = 0.0030 |\n| 604 | 1 | 0.578 | 0.023 | 18.548 | Neg. p = 0.0000 |\n| 605 | 1 | 0.857 | 0.153 | 7.943 | Neg. p = 0.0048 |\n","start_time":"2018-03-27T20:41:03.000Z","results":"{\n \"analysis\":{\n \"info\":\"FEL (Fixed Effects Likelihood)\\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\\n The estimates aggregate information over all branches,\\n so the signal is derived from\\n pervasive diversification or conservation. A subset of branches can be selected\\n for testing as well, in which case an additional (nuisance) parameter will be\\n inferred -- the non-synonymous rate on branches NOT selected for testing.\\n Multiple partitions within a NEXUS file are also supported\\n for recombination - aware analysis.\\n \",\n \"version\":\"2.00\",\n \"citation\":\"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222\",\n \"authors\":\"Sergei L Kosakovsky Pond and Simon DW Frost\",\n \"contact\":\"spond@temple.edu\",\n \"requirements\":\"in-frame codon alignment and a phylogenetic tree\"\n },\n \"input\":{\n \"file name\":\"/home/datamonkey/datamonkey-js-test/app/fel/output/5abaac4d149bf22529323b1f\",\n \"number of sequences\":23,\n \"number of sites\":610,\n \"partition count\":1,\n \"trees\":{\n \"0\":\"((((((X83276_1:0.0201128,CP004741:0.0179161)Node5:0.226388,FUGC01000:0.266796)Node4:0.0640335,(DS480414:0.00162187,XM_001644:0.00457919)Node9:0.350745)Node3:0.123853,(((XM_459150:0.0885372,XM_015610:0.0754118)Node14:0.211372,XM_020191:0.353467)Node13:0.0321712,(XM_001382:0.324562,(MCFD01000:0.29113,(KL411544:0.442128,(XM_016731:0.295293,KL657804:0.251789)Node24:0.129145)Node22:0.0301084)Node20:0.101123)Node18:0.0199704)Node12:0.0224006)Node2:0.0213305,(XM_455325:0.392946,AB093505:0.455559)Node27:0.08197)Node1:0.0320175,((XM_001527:0.352694,(XM_002547:0.268008,BDGI01000:0.256158)Node33:0.0183487)Node31:0.0845025,MPUK01000:0.438066)Node30:0.00638554,(XM_022605:0.302868,((XM_003683:0.243105,AB093510:0.327764)Node40:0.033475,AB093507:0.268639)Node39:0.0274843)Node37:0.0745136)\"\n }\n },\n \"fits\":{\n \"Nucleotide GTR\":{\n \"Log Likelihood\":-31399.51725131245,\n \"estimated parameters\":51,\n \"AIC-c\":62901.41395605171,\n \"Equilibrium frequencies\":[\n [0.2735388453314326],\n [0.2157578997386553],\n [0.2284925160370634],\n [0.2822107388928486]\n ],\n \"Rate Distributions\":{\n \"Substitution rate from nucleotide A to nucleotide C\":0.8226759799686492,\n \"Substitution rate from nucleotide A to nucleotide G\":1,\n \"Substitution rate from nucleotide A to nucleotide T\":0.5358871401241125,\n \"Substitution rate from nucleotide C to nucleotide G\":0.4960747078151422,\n \"Substitution rate from nucleotide C to nucleotide T\":1.186914439694899,\n \"Substitution rate from nucleotide G to nucleotide T\":0.3461540856360265\n },\n \"display order\":0\n },\n \"Global MG94xREV\":{\n \"Log Likelihood\":-30041.71302598351,\n \"estimated parameters\":58,\n \"AIC-c\":60083.42605196701,\n \"Equilibrium frequencies\":[\n [0.0231531443136123],\n [0.02141692300328506],\n [0.01777209595154855],\n [0.03288862316338764],\n [0.01547504170094581],\n [0.01431459036805327],\n [0.01187846981983051],\n [0.02198201713107667],\n [0.01205797599862802],\n [0.01115376555512796],\n [0.009255568208206482],\n [0.01712813704093299],\n [0.01760658826623624],\n [0.01628629529280953],\n [0.0135146212457629],\n [0.02500984051400417],\n [0.01429352343108977],\n [0.01322167247017603],\n [0.01097154954256847],\n [0.0203036917765758],\n [0.009553470066677529],\n [0.008837068955335299],\n [0.007333137322321232],\n [0.01357053161634443],\n [0.007443954917457078],\n [0.006885743342141768],\n [0.005713896966221974],\n [0.01057400346187777],\n [0.01086937387493588],\n [0.01005429501152281],\n [0.00834321044356145],\n [0.01543974920004995],\n [0.02738286799870513],\n [0.0253294657344918],\n [0.02101878478835645],\n [0.03889686923485048],\n [0.01830209402367534],\n [0.01692964606424913],\n [0.01404848372632435],\n [0.02599779387595566],\n [0.01426078292562034],\n [0.01319138712857277],\n [0.01094641829487168],\n [0.02025718448011629],\n [0.02082304139219865],\n [0.0192615511807069],\n [0.01598353487598005],\n [0.02957875406412981],\n [0.02006170373559971],\n [0.03080749807404455],\n [0.01449581258021081],\n [0.01340879224416622],\n [0.01112682444257515],\n [0.02059103985791493],\n [0.01044797798773389],\n [0.008669894702856838],\n [0.01604430341395179],\n [0.01649247922018204],\n [0.01525573169706596],\n [0.01265944353863297],\n [0.02342726874395498]\n ],\n \"Rate Distributions\":{\n \"non-synonymous/synonymous rate ratio for *test*\":[\n [0.1981994227647018, 1]\n ]\n },\n \"display order\":1\n }\n },\n \"timers\":{\n \"Total time\":{\n \"timer\":2290,\n \"order\":0\n },\n \"Model fitting\":{\n \"timer\":132,\n \"order\":1\n },\n \"FEL analysis\":{\n \"timer\":2157,\n \"order\":2\n }\n },\n \"tested\":{\n \"0\":{\n \"X83276_1\":\"test\",\n \"CP004741\":\"test\",\n \"Node5\":\"test\",\n \"FUGC01000\":\"test\",\n \"Node4\":\"test\",\n \"DS480414\":\"test\",\n \"XM_001644\":\"test\",\n \"Node9\":\"test\",\n \"Node3\":\"test\",\n \"XM_459150\":\"test\",\n \"XM_015610\":\"test\",\n \"Node14\":\"test\",\n \"XM_020191\":\"test\",\n \"Node13\":\"test\",\n \"XM_001382\":\"test\",\n \"MCFD01000\":\"test\",\n \"KL411544\":\"test\",\n \"XM_016731\":\"test\",\n \"KL657804\":\"test\",\n \"Node24\":\"test\",\n \"Node22\":\"test\",\n \"Node20\":\"test\",\n \"Node18\":\"test\",\n \"Node12\":\"test\",\n \"Node2\":\"test\",\n \"XM_455325\":\"test\",\n \"AB093505\":\"test\",\n \"Node27\":\"test\",\n \"Node1\":\"test\",\n \"XM_001527\":\"test\",\n \"XM_002547\":\"test\",\n \"BDGI01000\":\"test\",\n \"Node33\":\"test\",\n \"Node31\":\"test\",\n \"MPUK01000\":\"test\",\n \"Node30\":\"test\",\n \"XM_022605\":\"test\",\n \"XM_003683\":\"test\",\n \"AB093510\":\"test\",\n \"Node40\":\"test\",\n \"AB093507\":\"test\",\n \"Node39\":\"test\",\n \"Node37\":\"test\"\n }\n },\n \"data partitions\":{\n \"0\":{\n \"name\":\"fel.filter.default\",\n \"coverage\":[\n [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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name\":\"CP004741\",\n \"Nucleotide GTR\":0.01508000675987075,\n \"Global MG94xREV\":0.01122708142665916\n },\n \"XM_455325\":{\n \"original name\":\"XM_455325\",\n \"Nucleotide GTR\":0.4106545821972568,\n \"Global MG94xREV\":0.578314835594092\n },\n \"XM_001527\":{\n \"original name\":\"XM_001527\",\n \"Nucleotide GTR\":0.4523333206436111,\n \"Global MG94xREV\":0.6466228552683961\n },\n \"DS480414\":{\n \"original name\":\"DS480414\",\n \"Nucleotide GTR\":0.001250410481071279,\n \"Global MG94xREV\":0.001831493272240935\n },\n \"XM_459150\":{\n \"original name\":\"XM_459150\",\n \"Nucleotide GTR\":0.08141097500166343,\n \"Global MG94xREV\":0.09041182972545903\n },\n \"XM_001382\":{\n \"original name\":\"XM_001382\",\n \"Nucleotide GTR\":0.2831559951470788,\n \"Global MG94xREV\":0.4574536027818445\n },\n \"XM_001644\":{\n \"original name\":\"XM_001644\",\n \"Nucleotide GTR\":0.005067948690487577,\n \"Global MG94xREV\":0.005022522856206197\n },\n \"XM_002547\":{\n \"original name\":\"XM_002547\",\n \"Nucleotide GTR\":0.2925489270508604,\n \"Global MG94xREV\":0.4148405100279616\n },\n \"FUGC01000\":{\n \"original name\":\"FUGC01000\",\n \"Nucleotide GTR\":0.2777734582212519,\n \"Global MG94xREV\":0.3731899608852872\n },\n \"MCFD01000\":{\n \"original name\":\"MCFD01000\",\n \"Nucleotide GTR\":0.2765178585650078,\n \"Global MG94xREV\":0.384232507570769\n },\n \"KL411544\":{\n \"original name\":\"KL411544\",\n \"Nucleotide GTR\":0.513813123674987,\n \"Global MG94xREV\":0.7558768508575046\n },\n \"XM_015610\":{\n \"original name\":\"XM_015610\",\n \"Nucleotide GTR\":0.08166858776742557,\n \"Global MG94xREV\":0.09533136846006064\n },\n \"XM_020191\":{\n \"original name\":\"XM_020191\",\n \"Nucleotide GTR\":0.3790235852990241,\n \"Global MG94xREV\":0.5345755321035673\n },\n \"XM_016731\":{\n \"original name\":\"XM_016731\",\n \"Nucleotide GTR\":0.2266792787944671,\n \"Global MG94xREV\":0.2825121445107009\n },\n \"KL657804\":{\n \"original name\":\"KL657804\",\n \"Nucleotide GTR\":0.3108150599636745,\n \"Global MG94xREV\":0.380085852914567\n },\n \"BDGI01000\":{\n \"original name\":\"BDGI01000\",\n \"Nucleotide GTR\":0.2551971781467891,\n \"Global MG94xREV\":0.354151908137475\n },\n \"XM_022605\":{\n \"original name\":\"XM_022605\",\n \"Nucleotide GTR\":0.3010341712575952,\n \"Global MG94xREV\":0.3407324200827355\n },\n \"XM_003683\":{\n \"original name\":\"XM_003683\",\n \"Nucleotide GTR\":0.223389675820111,\n \"Global MG94xREV\":0.3078522842282945\n },\n \"MPUK01000\":{\n \"original name\":\"MPUK01000\",\n \"Nucleotide GTR\":0.4631055579675414,\n \"Global MG94xREV\":0.7238920127651389\n },\n \"AB093507\":{\n \"original name\":\"AB093507\",\n \"Nucleotide GTR\":0.2632678895041553,\n \"Global MG94xREV\":0.3160406237355088\n },\n \"AB093510\":{\n \"original name\":\"AB093510\",\n \"Nucleotide GTR\":0.3980773373094048,\n \"Global MG94xREV\":0.6159575534668678\n },\n \"AB093505\":{\n \"original name\":\"AB093505\",\n \"Nucleotide GTR\":0.4964092801407045,\n \"Global MG94xREV\":0.7693921136267091\n },\n \"Node1\":{\n \"Nucleotide GTR\":0.1073023501156848,\n \"Global MG94xREV\":0.1868898431774864\n },\n \"Node12\":{\n \"Nucleotide GTR\":0.07873906812036577,\n \"Global MG94xREV\":0.1013869727866173\n },\n \"Node13\":{\n \"Nucleotide GTR\":0.1057041945817754,\n \"Global MG94xREV\":0.1717630910745506\n },\n \"Node14\":{\n \"Nucleotide GTR\":0.2560273345117812,\n \"Global MG94xREV\":0.4137126921437162\n },\n \"Node18\":{\n \"Nucleotide GTR\":0.05446798709729882,\n \"Global MG94xREV\":0.04140272023732599\n },\n \"Node2\":{\n \"Nucleotide GTR\":0.00890457438125021,\n \"Global MG94xREV\":0.01825346539956163\n },\n \"Node20\":{\n \"Nucleotide GTR\":0.1964561050157351,\n \"Global MG94xREV\":0.1936052603091895\n },\n \"Node22\":{\n \"Nucleotide GTR\":0.07208609976309405,\n \"Global MG94xREV\":0.1098863676467544\n },\n \"Node24\":{\n \"Nucleotide GTR\":0.156758519765105,\n \"Global MG94xREV\":0.2433404752668564\n },\n \"Node27\":{\n \"Nucleotide GTR\":0.2435160216829575,\n \"Global MG94xREV\":0.3880845302208268\n },\n \"Node3\":{\n \"Nucleotide GTR\":0.2232927249597996,\n \"Global MG94xREV\":0.3623636393030356\n },\n \"Node30\":{\n \"Nucleotide GTR\":0.06794839174087069,\n \"Global MG94xREV\":0.119790314580251\n },\n \"Node31\":{\n \"Nucleotide GTR\":0.1343199498788741,\n \"Global MG94xREV\":0.2234309136255851\n },\n \"Node33\":{\n \"Nucleotide GTR\":0.01624040873359438,\n \"Global MG94xREV\":0.02620610711917259\n },\n \"Node37\":{\n \"Nucleotide GTR\":0.138504865137844,\n \"Global MG94xREV\":0.2381180054746817\n },\n \"Node39\":{\n \"Nucleotide GTR\":0.07620260795851688,\n \"Global MG94xREV\":0.1358902775907355\n },\n \"Node4\":{\n \"Nucleotide GTR\":0.0429123381569244,\n \"Global MG94xREV\":0.05634011682431887\n },\n \"Node40\":{\n \"Nucleotide GTR\":0.06255997442868282,\n \"Global MG94xREV\":0.1021701756888928\n },\n \"Node5\":{\n \"Nucleotide GTR\":0.2249758794508632,\n \"Global MG94xREV\":0.2850067260022524\n },\n \"Node9\":{\n \"Nucleotide GTR\":0.4375698669267103,\n \"Global MG94xREV\":0.6439732718075979\n }\n },\n \"attributes\":{\n \"original name\":{\n \"attribute type\":\"node label\",\n \"display order\":-1\n },\n \"Nucleotide GTR\":{\n \"attribute type\":\"branch length\",\n \"display order\":0\n },\n \"Global MG94xREV\":{\n \"attribute type\":\"branch length\",\n \"display order\":1\n }\n }\n },\n \"MLE\":{\n \"headers\":[\n [\"alpha\", \"Synonymous substitution rate at a site\"],\n [\"beta\", \"Non-synonymous substitution rate at a site\"],\n [\"alpha=beta\", \"The rate estimate under the neutral model\"],\n [\"LRT\", \"Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha\"],\n [\"p-value\", \"Likelihood ration test statistic for beta = alpha, versus beta &neq; alpha\"],\n [\"Total branch length\", \"The total length of branches contributing to inference at this site, and used to scale dN-dS\"]\n ],\n \"content\":{\n \"0\":[\n 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