annotate test-data/BUSTED/gene1.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

{
 "Evidence Ratios":{
  },
 "Site Log Likelihood":{
   "unconstrained":    [
[-3.290019315059098, -4.175663627535955, -4.175663627535955, -4.173115241795732, -9.238614141422939, -6.201388047751721, -3.588161705747214, -3.846065275733122, -11.6279127051655, -4.374967447338868, -4.667251719415955, -5.369450552211644, -4.609545779703736, -4.521369648345189, -3.290019315059098, -4.472687242532417, -3.396709886941963, -5.214702609387182, -4.561720576655006, -3.577740971164724, -4.175663627535955, -5.214702609387182, -4.169795185009985, -4.22785259313233, -4.775958986232662, -11.23524464752527, -14.05898845363783, -4.364741485582735, -4.188622564988608, -4.561720576655006, -3.588161705747214, -3.577740971164724, -4.609545779703736, -4.22785259313233, -10.80905338405208, -4.290623032758742, -4.188622564988608, -9.102696648764709, -10.15065862754325, -5.109026588357197, -7.639966748483763, -4.290623032758742, -5.27139973585393, -3.290019315059098, -3.396709886941963, -15.39005248416766, -4.169795185009985, -3.290019315059098, -5.490588024798257, -8.79815567312038, -3.128919286251878, -4.354491537508268, -4.609545779703736, -4.273615502328157, -3.577740971164724, -7.949833968989759, -4.273615502328157, -5.166376479360413, -3.128919286251878, -9.523238743964589, -4.460708940557628, -3.638165346693491, -4.354491537508268, -7.804776345656695, -4.358412699477345, -4.188622564988608, -5.490588024798257, -3.577740971164724, -4.171027191490039, -11.91661958005109, -4.22785259313233, -4.609545779703736, -3.588161705747214, -3.588161705747214, -4.521369648345189, -4.290623032758742, -4.561720576655006, -4.032579906673688, -3.396709886941963, -4.169795185009985, -11.49141288792201, -4.628717534587926, -5.434467285003718, -9.922930097774541, -6.229068584733115, -3.396709886941963, -6.925748094379387, -4.032579906673688, -4.22785259313233, -4.346914805883308, -3.290019315059098, -8.47331136085584, -6.844904286989593, -3.128919286251878, -3.290019315059098, -6.844904286989593, -6.396159179643725, -3.768797718390692, -3.396709886941963, -3.577740971164724]
    ]
  },
 "Synonymous site-posteriors":  [
[0.3794119907403843, 0.4267595406129572, 0.4267595406129572, 0.4063808428796526, 0, 0, 0.4217848486529984, 0.4568444577350967, 0, 0.423080649210957, 0.4736963110223841, 0.4975948898723052, 0.4510648306173076, 0.4505742158238857, 0.3794119907403843, 0.5647186201699436, 0.4098734284649755, 0.4681162016838413, 0.4652430687753451, 0.4179238939393959, 0.4267595406129572, 0.4681162016838413, 0.4553016881818676, 0.4450442300667967, 0.4864120983399342, 0, 0, 0.418263713562334, 0.5266121996835147, 0.4652430687753451, 0.4217848486529984, 0.4179238939393959, 0.4510648306173076, 0.4450442300667967, 0, 0.4244283159073019, 0.5266121996835147, 0, 0, 0.4596959332621445, 0, 0.4244283159073019, 0.4873282341404275, 0.3794119907403843, 0.4098734284649755, 0, 0.4553016881818676, 0.3794119907403843, 0.4948461770719139, 0, 0.38005938078955, 0.4450273902905073, 0.4510648306173076, 0.544604978932537, 0.4179238939393959, 0, 0.544604978932537, 0.4788748786614854, 0.38005938078955, 0, 0.4534243838082746, 0.4367006382093872, 0.4450273902905073, 0, 0.4639772686656731, 0.5266121996835147, 0.4948461770719139, 0.4179238939393959, 0.3632238073882605, 0, 0.4450442300667967, 0.4510648306173076, 0.4217848486529984, 0.4217848486529984, 0.4505742158238857, 0.4244283159073019, 0.4652430687753451, 0.4482749189029647, 0.4098734284649755, 0.4553016881818676, 0, 0.4633617354560431, 0.4756118206653533, 0, 0, 0.4098734284649755, 0, 0.4482749189029647, 0.4450442300667967, 0.4309067696768855, 0.3794119907403843, 0, 0, 0.38005938078955, 0.3794119907403843, 0, 0, 0.4298993958551496, 0.4098734284649755, 0.4179238939393959],
  [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
  [0.6205880092596157, 0.5732404593870428, 0.5732404593870428, 0.5936191571203474, 1, 1, 0.5782151513470016, 0.5431555422649033, 0.9999999999999999, 0.5769193507890429, 0.5263036889776157, 0.5024051101276948, 0.5489351693826925, 0.5494257841761142, 0.6205880092596157, 0.4352813798300565, 0.5901265715350245, 0.5318837983161587, 0.534756931224655, 0.582076106060604, 0.5732404593870428, 0.5318837983161587, 0.5446983118181324, 0.5549557699332032, 0.5135879016600658, 1, 1, 0.581736286437666, 0.4733878003164854, 0.534756931224655, 0.5782151513470016, 0.582076106060604, 0.5489351693826925, 0.5549557699332032, 1, 0.575571684092698, 0.4733878003164854, 1, 1, 0.5403040667378556, 0.9999999999999999, 0.575571684092698, 0.5126717658595725, 0.6205880092596157, 0.5901265715350245, 1, 0.5446983118181324, 0.6205880092596157, 0.5051538229280861, 0.9999999999999999, 0.6199406192104499, 0.5549726097094927, 0.5489351693826925, 0.455395021067463, 0.582076106060604, 1, 0.455395021067463, 0.5211251213385146, 0.6199406192104499, 1, 0.5465756161917255, 0.5632993617906127, 0.5549726097094927, 0.9999999999999999, 0.5360227313343269, 0.4733878003164854, 0.5051538229280861, 0.582076106060604, 0.6367761926117396, 1, 0.5549557699332032, 0.5489351693826925, 0.5782151513470016, 0.5782151513470016, 0.5494257841761142, 0.575571684092698, 0.534756931224655, 0.5517250810970353, 0.5901265715350245, 0.5446983118181324, 1, 0.5366382645439569, 0.5243881793346465, 1, 1, 0.5901265715350245, 1, 0.5517250810970353, 0.5549557699332032, 0.5690932303231144, 0.6205880092596157, 1, 0.9999999999999999, 0.6199406192104499, 0.6205880092596157, 0.9999999999999999, 1, 0.5701006041448504, 0.5901265715350245, 0.582076106060604]
  ],
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond",
   "citation":"*Gene-wide identification of episodic selection*, Mol Biol Evol. 32(5):1365-71, *Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril*, Mol Biol Evol. 37(8):2430-2439",
   "contact":"[e-mail]",
   "info":"BUSTED (branch-site unrestricted statistical test of episodic diversification) uses a random effects branch-site model fitted  jointly to all or a subset of tree branches in order to test for alignment-wide evidence of episodic diversifying selection. Assuming there is evidence of positive selection (i.e. there is an omega > 1),  BUSTED will also perform a quick evidence-ratio style analysis to explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, and relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2).\n                               \nVersion 2.1 adds a grid search for the initial starting point.\n\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. \n\nVersion 3.0 implements the option for branch-site variation in synonymous substitution rates. \n\nVersion 3.1 adds HMM auto-correlation option for SRV, and binds SRV distributions for multiple branch sets.\n\nVersion 4.0 adds support for multiple hits (MH), ancestral state reconstruction saved to JSON, and profiling of branch-site level support for selection / multiple hits.\n\nVersion 4.2 adds calculation of MH-attributable fractions of substitutions.\n\nVersion 4.5 adds an 'error absorption' component \n\nVersion 4.6 adds support for MSS-type models\n",
   "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})",
   "settings":{
     "error-sink":1,
     "mss":"No",
     "multiple-hit":"None",
     "srv":"Yes"
    },
   "version":"4.6"
  },
 "background":1,
 "branch attributes":{
   "0":{
     "Node3":{
       "MG94xREV with separate rates for branch sets":0.007049012269592678,
       "Nucleotide GTR":0.007289662052004695,
       "Posterior prob omega class":        [
[0],
        [0.9353670953035417],
        [0.06461204144565623],
        [2.086325080203871e-05]
        ],
       "Posterior prob omega class by site":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
        [0.9151977400221446, 0.9149330883022148, 0.9149330883022148, 0.9148696121842339, 0.9153337079073738, 0.9150133383802144, 0.914918356005114, 0.9151067827328278, 0.9155494332711233, 0.9148834586751281, 0.9152482098936171, 0.9151769259450234, 0.9151603730030921, 0.9149105824312139, 0.9151977400221446, 0.9149347410382047, 0.9149058352505537, 0.9150768845566132, 0.9151779964037902, 0.91493806192132, 0.9149330883022148, 0.9150768845566132, 0.9150932222217523, 0.9151955058905722, 0.9150874243839585, 0.9153792259695116, 0.9035057859858112, 0.9148829947873742, 0.9149560466789169, 0.9151779964037902, 0.914918356005114, 0.91493806192132, 0.9151603730030921, 0.9151955058905722, 0.915013337678751, 0.9150022812196591, 0.9149560466789169, 0.9155258105428431, 0.915551930707027, 0.9150026548692872, 0.9149777488992396, 0.9150022812196591, 0.9152353219326763, 0.9151977400221446, 0.9149058352505537, 0.9151730477564946, 0.9150932222217523, 0.9151977400221446, 0.9151543617933064, 0.9154817642412356, 0.9151542360454418, 0.9151941362509409, 0.9151603730030921, 0.914943220022795, 0.91493806192132, 0.9154965359394003, 0.914943220022795, 0.9151671130018076, 0.9151542360454418, 0.915695648875959, 0.9152673587384784, 0.9151199779760567, 0.9151941362509409, 0.91521660015107, 0.9150327491492556, 0.9149560466789169, 0.9151543617933064, 0.91493806192132, 0.9150188646240174, 0.9152167114228641, 0.9151955058905722, 0.9151603730030921, 0.914918356005114, 0.914918356005114, 0.9149105824312139, 0.9150022812196591, 0.9151779964037902, 0.9150407400799804, 0.9149058352505537, 0.9150932222217523, 0.9151730261854838, 0.9150640099362826, 0.9149952436603092, 0.9154967126403919, 0.9150403943541737, 0.9149058352505537, 0.9151284171511251, 0.9150407400799804, 0.9151955058905722, 0.9149729632599457, 0.9151977400221446, 0.9151730903365141, 0.9150414083351168, 0.9151542360454418, 0.9151977400221446, 0.9150414083351168, 0.9150723309457811, 0.9149496264068151, 0.9149058352505537, 0.91493806192132],
        [0.0843528066788021, 0.08460406214800659, 0.08460406214800659, 0.08466421098413629, 0.08422421764776274, 0.08452810261752025, 0.08461801738563114, 0.0844391399399098, 0.08401926472605259, 0.08465109860929841, 0.0843046907600772, 0.08437239852281651, 0.08438816288149432, 0.08462537841537243, 0.0843528066788021, 0.08460231543630754, 0.08462987896767399, 0.0844676013223663, 0.08437152021742182, 0.08459935126485479, 0.08460406214800659, 0.0844676013223663, 0.08445201091544316, 0.08435480480756226, 0.08445749372889229, 0.08418085546493023, 0.0954623038997045, 0.08465153819560495, 0.08458211940918406, 0.08437152021742182, 0.08461801738563114, 0.08459935126485479, 0.08438816288149432, 0.08435480480756226, 0.0845281032856763, 0.08453849175371264, 0.08458211940918406, 0.08404150487529673, 0.08401669780405847, 0.08453812134719381, 0.08456185671405114, 0.08453849175371264, 0.08431692014522334, 0.0843528066788021, 0.08462987896767399, 0.08437644718797066, 0.08445201091544316, 0.0843528066788021, 0.08439393431459691, 0.08408326382873119, 0.08439410257545127, 0.08435621384487543, 0.08438816288149432, 0.0845942789915294, 0.08459935126485479, 0.0840693009988186, 0.0845942789915294, 0.08438184159129572, 0.08439410257545127, 0.08388014166331975, 0.08428652125898915, 0.08442662908245631, 0.08435621384487543, 0.0843354917790068, 0.084509375346993, 0.08458211940918406, 0.08439393431459691, 0.08459935126485479, 0.08452268826127904, 0.08433538636531261, 0.08435480480756226, 0.08438816288149432, 0.08461801738563114, 0.08461801738563114, 0.08462537841537243, 0.08453849175371264, 0.08437152021742182, 0.084501799934938, 0.08462987896767399, 0.08445201091544316, 0.0843764675741874, 0.0844798174950419, 0.08454514056320835, 0.0840691341060654, 0.08450247441767141, 0.08462987896767399, 0.08441908339158098, 0.084501799934938, 0.08435480480756226, 0.08456627654891793, 0.0843528066788021, 0.08437640630840616, 0.08450151658182631, 0.08439410257545127, 0.0843528066788021, 0.08450151658182631, 0.08447222210001473, 0.08458839074399647, 0.08462987896767399, 0.08459935126485479],
        [0.0004494532990532372, 0.0004628495497787002, 0.0004628495497787002, 0.0004661768316297815, 0.0004420744448635032, 0.0004585590022653273, 0.000463626609254869, 0.0004540773272625013, 0.0004313020028241371, 0.000465442715573365, 0.0004470993463056758, 0.0004506755321599876, 0.0004514641154136901, 0.0004640391534136732, 0.0004494532990532372, 0.0004629435254877354, 0.0004642857817722715, 0.0004555141210204983, 0.0004504833787881711, 0.0004625868138251854, 0.0004628495497787002, 0.0004555141210204983, 0.0004547668628045192, 0.0004496893018654913, 0.0004550818871491933, 0.000439918565558052, 0.001031910114484335, 0.0004654670170208092, 0.0004618339118989882, 0.0004504833787881711, 0.000463626609254869, 0.0004625868138251854, 0.0004514641154136901, 0.0004496893018654913, 0.0004585590355726647, 0.0004592270266282789, 0.0004618339118989882, 0.0004326845818601744, 0.000431371488914473, 0.0004592237835188933, 0.0004603943867092644, 0.0004592270266282789, 0.0004477579221004922, 0.0004494532990532372, 0.0004642857817722715, 0.000450505055534887, 0.0004547668628045192, 0.0004494532990532372, 0.0004517038920965988, 0.0004349719300331834, 0.0004516613791069996, 0.0004496499041836278, 0.0004514641154136901, 0.0004625009856755743, 0.0004625868138251854, 0.0004341630617810997, 0.0004625009856755743, 0.0004510454068966126, 0.0004516613791069996, 0.00042420946072127, 0.0004461200025324903, 0.0004533929414869307, 0.0004496499041836278, 0.0004479080699232817, 0.0004578755037514242, 0.0004618339118989882, 0.0004517038920965988, 0.0004625868138251854, 0.0004584471147036225, 0.0004479022118232207, 0.0004496893018654913, 0.0004514641154136901, 0.000463626609254869, 0.000463626609254869, 0.0004640391534136732, 0.0004592270266282789, 0.0004504833787881711, 0.0004574599850816045, 0.0004642857817722715, 0.0004547668628045192, 0.0004505062403288287, 0.0004561725686755511, 0.0004596157764825212, 0.0004341532535427586, 0.0004571312281549848, 0.0004642857817722715, 0.0004524994572938475, 0.0004574599850816045, 0.0004496893018654913, 0.0004607601911362361, 0.0004494532990532372, 0.0004505033550797285, 0.0004570750830569257, 0.0004516613791069996, 0.0004494532990532372, 0.0004570750830569257, 0.0004554469542041989, 0.0004619828491883951, 0.0004642857817722715, 0.0004625868138251854]
        ],
       "unconstrained":0.006866927675951353
      },
     "Node4":{
       "MG94xREV with separate rates for branch sets":0.01560819603098484,
       "Nucleotide GTR":0.01388744473547059,
       "Posterior prob omega class":        [
[0],
        [0.9700134742693405],
        [0.02998649797196691],
        [2.77586925402575e-08]
        ],
       "Posterior prob omega class by site":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
        [0.9158777632193089, 0.9152140735301014, 0.9152140735301014, 0.9150533189945288, 0.9160630531000094, 0.9154185729056845, 0.9151766293411721, 0.9156491021126465, 0.9167535577249423, 0.9150887832757459, 0.9160026499873604, 0.9158234175600194, 0.9157819290216459, 0.9151569360072535, 0.9158777632193089, 0.9152147829832338, 0.9151448611487456, 0.9155757881598283, 0.9158285190626677, 0.9152267606622403, 0.9152140735301014, 0.9155757881598283, 0.9156149786276654, 0.915870544031687, 0.9156003267632836, 0.9163219612121846, 0.9163827188866879, 0.9150873337163578, 0.915268555029165, 0.9158285190626677, 0.9151766293411721, 0.9152267606622403, 0.9157819290216459, 0.915870544031687, 0.9154183794269476, 0.9153897161556438, 0.915268555029165, 0.9167021785197577, 0.9167683125840838, 0.915390480569593, 0.9152942443845983, 0.9153897161556438, 0.9159700422060851, 0.9158777632193089, 0.9151448611487456, 0.9158120827123243, 0.9156149786276654, 0.9158777632193089, 0.9157688728103833, 0.9166260609811728, 0.9157680916223574, 0.9158692508947182, 0.9157819290216459, 0.9152360784219746, 0.9152267606622403, 0.9165946875067987, 0.9152360784219746, 0.9158010528061127, 0.9157680916223574, 0.9171287691003759, 0.9160508532976659, 0.9156824535773247, 0.9158692508947182, 0.9158980006045139, 0.9154622168064745, 0.915268555029165, 0.9157688728103833, 0.9152267606622403, 0.9154297485495306, 0.9159081161475103, 0.915870544031687, 0.9157819290216459, 0.9151766293411721, 0.9151766293411721, 0.9151569360072535, 0.9153897161556438, 0.9158285190626677, 0.9154823835011858, 0.9151448611487456, 0.9156149786276654, 0.9158158182531743, 0.9155429557093289, 0.9153716485941472, 0.9166290066765946, 0.9154868872989199, 0.9151448611487456, 0.9157109976296158, 0.9154823835011858, 0.915870544031687, 0.9153152711066849, 0.9158777632193089, 0.915825014829628, 0.9154900101185053, 0.9157680916223574, 0.9158777632193089, 0.9154900101185053, 0.9155685046687553, 0.9152560511502645, 0.9151448611487456, 0.9152267606622403],
        [0.0837036529025873, 0.0843372094968256, 0.0843372094968256, 0.0844899991101801, 0.08352954143686661, 0.08414336447931257, 0.08437276730206893, 0.08392177303324515, 0.08286963013355045, 0.08445634179186758, 0.08358328074921932, 0.08375454674799707, 0.0837944472023492, 0.08439145390682155, 0.0837036529025873, 0.08433545019923228, 0.08440294335660289, 0.08399221226883882, 0.08375045219122879, 0.08432516170044255, 0.0843372094968256, 0.08399221226883882, 0.08395435334055872, 0.08370981985153944, 0.08396818572571203, 0.08328163485199501, 0.08322316179719648, 0.08445772494561829, 0.08428430060092877, 0.08375045219122879, 0.08437276730206893, 0.08432516170044255, 0.0837944472023492, 0.08370981985153944, 0.08414354915438073, 0.0841702405965631, 0.08428430060092877, 0.08291768057831368, 0.08285447012580494, 0.0841694137434968, 0.08426151270964843, 0.0841702405965631, 0.08361437591981502, 0.0837036529025873, 0.08440294335660289, 0.08376747451720325, 0.08395435334055872, 0.0837036529025873, 0.08380724740084235, 0.0829903567585097, 0.08380829942246928, 0.08371166727441094, 0.0837944472023492, 0.08431519980459284, 0.08432516170044255, 0.08302017015543071, 0.08431519980459284, 0.08377660559674273, 0.08380829942246928, 0.08250978293684526, 0.08353732601356564, 0.08389003145910283, 0.08371166727441094, 0.08368772045621546, 0.0840998870663531, 0.08428430060092877, 0.08380724740084235, 0.08432516170044255, 0.08413168164376066, 0.0836780761630674, 0.08370981985153944, 0.0837944472023492, 0.08437276730206893, 0.08437276730206893, 0.08439145390682155, 0.0841702405965631, 0.08375045219122879, 0.08408070104093504, 0.08440294335660289, 0.08395435334055872, 0.08376391570529539, 0.08402349243218464, 0.08418729059248077, 0.08298755705970334, 0.08407849473510264, 0.08440294335660289, 0.08386559716300945, 0.08408070104093504, 0.08370981985153944, 0.0842410211195062, 0.0837036529025873, 0.08375502533671321, 0.0840755465759926, 0.08380829942246928, 0.0837036529025873, 0.0840755465759926, 0.08400098360367797, 0.08429730954162383, 0.08440294335660289, 0.08432516170044255],
        [0.0004185838781038405, 0.0004487169730730625, 0.0004487169730730625, 0.0004566818952910347, 0.0004074054631239655, 0.000438062615002927, 0.0004506033567589024, 0.0004291248541083581, 0.0003768121415073204, 0.000454874932386434, 0.0004140692634202725, 0.0004220356919835314, 0.0004236237760048757, 0.0004516100859249172, 0.0004185838781038405, 0.0004497668175339122, 0.0004521954946515376, 0.0004319995713327992, 0.0004210287461033698, 0.0004480776373170959, 0.0004487169730730625, 0.0004319995713327992, 0.0004306680317759179, 0.0004196361167736211, 0.0004314875110044189, 0.0003964039358204074, 0.0003941193161156663, 0.0004549413380238684, 0.0004471443699062045, 0.0004210287461033698, 0.0004506033567589024, 0.0004480776373170959, 0.0004236237760048757, 0.0004196361167736211, 0.0004380714186716248, 0.0004400432477931076, 0.0004471443699062045, 0.0003801409019287692, 0.0003772172901114082, 0.0004401056869101767, 0.0004442429057532444, 0.0004400432477931076, 0.0004155818740998857, 0.0004185838781038405, 0.0004521954946515376, 0.0004204427704725355, 0.0004306680317759179, 0.0004185838781038405, 0.0004238797887743086, 0.0003835822603173661, 0.0004236089551733093, 0.0004190818308709628, 0.0004236237760048757, 0.0004487217734325426, 0.0004480776373170959, 0.000385142337770659, 0.0004487217734325426, 0.0004223415971446163, 0.0004236089551733093, 0.000361447962778843, 0.0004118206887684664, 0.0004275149635724493, 0.0004190818308709628, 0.0004142789392706555, 0.0004378961271723892, 0.0004471443699062045, 0.0004238797887743086, 0.0004480776373170959, 0.0004385698067087048, 0.000413807689422235, 0.0004196361167736211, 0.0004236237760048757, 0.0004506033567589024, 0.0004506033567589024, 0.0004516100859249172, 0.0004400432477931076, 0.0004210287461033698, 0.0004369154578791491, 0.0004521954946515376, 0.0004306680317759179, 0.0004202660415303749, 0.000433551858486513, 0.0004410608133719652, 0.0003834362637020058, 0.0004346179659774826, 0.0004521954946515376, 0.0004234052073747308, 0.0004369154578791491, 0.0004196361167736211, 0.0004437077738089686, 0.0004185838781038405, 0.0004199598336588482, 0.0004344433055020568, 0.0004236089551733093, 0.0004185838781038405, 0.0004344433055020568, 0.0004305117275666993, 0.000446639308111617, 0.0004521954946515376, 0.0004480776373170959]
        ],
       "unconstrained":0.01758032741456334
      },
     "Node7":{
       "MG94xREV with separate rates for branch sets":0.006613847169003491,
       "Nucleotide GTR":0.006185828741026453,
       "Posterior prob omega class":        [
[0],
        [0.8400468103750708],
        [0.1597933209520157],
        [0.0001598686729135425]
        ],
       "Posterior prob omega class by site":        [
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
        [0.9152021971845653, 0.9149349147610991, 0.9149349147610991, 0.9148708034958959, 0.9153395349225428, 0.9150159704351355, 0.9149200347097585, 0.9151103346206012, 0.915557402455089, 0.9148847892616963, 0.9152531639739606, 0.9151811706622274, 0.9151644534408548, 0.914912183276865, 0.9152021971845653, 0.9149365754930456, 0.9149073884919511, 0.915080143299804, 0.9151822579798715, 0.9149399383100026, 0.9149349147610991, 0.915080143299804, 0.9150966389763264, 0.9151999365313818, 0.9150907831045731, 0.9153854987641886, 0.7678169282651872, 0.9148843203422605, 0.9149580938882588, 0.9151822579798715, 0.9149200347097585, 0.9149399383100026, 0.9151644534408548, 0.9151999365313818, 0.9150159697266409, 0.9150048008798459, 0.9149580938882588, 0.915533514553418, 0.9155599144798782, 0.9150051778235969, 0.9149800264234038, 0.9150048008798459, 0.9152401473702045, 0.9152021971845653, 0.9149073884919511, 0.9151772621678315, 0.9150966389763264, 0.9152021971845653, 0.9151583874568524, 0.9155029933325044, 0.9151582594456706, 0.9151985589293845, 0.9151644534408548, 0.9149451390137013, 0.9149399383100026, 0.9155039675531141, 0.9149451390137013, 0.9151712659435138, 0.9151582594456706, 0.9157050612060691, 0.915272503628435, 0.915123661666351, 0.9151985589293845, 0.9152212684382308, 0.915035561955223, 0.9149580938882588, 0.9151583874568524, 0.9149399383100026, 0.9150215451596324, 0.915221380944053, 0.9151999365313818, 0.9151644534408548, 0.9149200347097585, 0.9149200347097585, 0.914912183276865, 0.9150048008798459, 0.9151822579798715, 0.9150436326594128, 0.9149073884919511, 0.9150966389763264, 0.915177240063496, 0.9150671397360864, 0.9149976923018772, 0.9155041460095592, 0.9150432976011265, 0.9149073884919511, 0.9151322030208324, 0.9150436326594128, 0.9151999365313818, 0.9149751891835269, 0.9152021971845653, 0.9151773051837894, 0.9150443220142506, 0.9151582594456706, 0.9152021971845653, 0.9150443220142506, 0.9150755545668009, 0.9149516185388131, 0.9149073884919511, 0.9149399383100026],
        [0.08434856803751969, 0.08460233068710984, 0.08460233068710984, 0.08466308260699786, 0.08421868315275099, 0.08452560790616562, 0.08461642612215732, 0.08443576362556074, 0.08401168582662794, 0.08464983815305054, 0.08429997462436788, 0.08436835904628344, 0.08438428094120082, 0.08462386097993284, 0.08434856803751969, 0.08460057281246305, 0.08462840677617335, 0.08446450590319871, 0.08436746734854784, 0.08459757243336853, 0.08460233068710984, 0.08446450590319871, 0.0844487633542992, 0.08435058902514331, 0.08445430102382905, 0.08417489328909537, 0.2243930207398437, 0.08465028252224577, 0.08458017463055503, 0.08436746734854784, 0.08461642612215732, 0.08459757243336853, 0.08438428094120082, 0.08435058902514331, 0.08452560858102864, 0.08453610199770302, 0.08458017463055503, 0.08403417499921907, 0.08400910119429714, 0.0845357281385876, 0.08455969925372973, 0.08453610199770302, 0.08431232649363191, 0.08434856803751969, 0.08462840677617335, 0.08437244374590616, 0.0844487633542992, 0.08434856803751969, 0.08439010580467816, 0.08406315108125037, 0.08439027719575744, 0.0843520077634019, 0.08438428094120082, 0.08459245606243311, 0.08459757243336853, 0.08406223089938515, 0.08459245606243311, 0.08437789203656436, 0.08439027719575744, 0.08387118144694566, 0.08428162347216059, 0.0844231274769276, 0.0843520077634019, 0.08433106356281665, 0.08450670242304219, 0.08458017463055503, 0.08439010580467816, 0.08459757243336853, 0.08452014401264007, 0.08433095697900901, 0.08435058902514331, 0.08438428094120082, 0.08461642612215732, 0.08461642612215732, 0.08462386097993284, 0.08453610199770302, 0.08436746734854784, 0.08449905120013258, 0.08462840677617335, 0.0844487633542992, 0.08437246463646943, 0.08447684480563074, 0.08454281784544899, 0.08406206234147456, 0.08449972239641274, 0.08462840677617335, 0.08441549365987534, 0.08449905120013258, 0.08435058902514331, 0.0845641657741371, 0.08434856803751969, 0.08437240244507196, 0.08449875471651958, 0.08439027719575744, 0.08434856803751969, 0.08449875471651958, 0.08446916608144657, 0.08458650196892256, 0.08462840677617335, 0.08459757243336853],
        [0.0004492347779148642, 0.0004627545517909902, 0.0004627545517909902, 0.0004661138971062413, 0.0004417819247062532, 0.00045842165869894, 0.0004635391680841786, 0.0004539017538380798, 0.0004309117182831417, 0.0004653725852531466, 0.0004468614016715828, 0.0004504702914891563, 0.0004512656179442668, 0.000463955743202196, 0.0004492347779148642, 0.0004628516944913242, 0.0004642047318755908, 0.0004553507969972518, 0.0004502746715806909, 0.0004624892566288283, 0.0004627545517909902, 0.0004553507969972518, 0.0004545976693744218, 0.0004494744434748985, 0.0004549158715978459, 0.0004396079467160203, 0.007790050994969002, 0.0004653971354937609, 0.0004617314811862648, 0.0004502746715806909, 0.0004635391680841786, 0.0004624892566288283, 0.0004512656179442668, 0.0004494744434748985, 0.0004584216923304005, 0.0004590971224510614, 0.0004617314811862648, 0.0004323104473629174, 0.0004309843258246667, 0.0004590940378154909, 0.0004602743228664305, 0.0004590971224510614, 0.0004475261361635684, 0.0004492347779148642, 0.0004642047318755908, 0.0004502940862624636, 0.0004545976693744218, 0.0004492347779148642, 0.0004515067384694943, 0.0004338555862452296, 0.000451463358571992, 0.0004494333072135715, 0.0004512656179442668, 0.0004624049238656044, 0.0004624892566288283, 0.0004338015475006306, 0.0004624049238656044, 0.0004508420199217758, 0.000451463358571992, 0.0004237573469853164, 0.0004458728994043993, 0.0004532108567213617, 0.0004494333072135715, 0.0004476679989526213, 0.0004577356217347934, 0.0004617314811862648, 0.0004515067384694943, 0.0004624892566288283, 0.0004583108277275552, 0.000447662076937982, 0.0004494744434748985, 0.0004512656179442668, 0.0004635391680841786, 0.0004635391680841786, 0.000463955743202196, 0.0004590971224510614, 0.0004502746715806909, 0.0004573161404547224, 0.0004642047318755908, 0.0004545976693744218, 0.0004502953000345997, 0.0004560154582827481, 0.0004594898526739387, 0.0004337916489663086, 0.0004569800024608009, 0.0004642047318755908, 0.0004523033192922024, 0.0004573161404547224, 0.0004494744434748985, 0.0004606450423359562, 0.0004492347779148642, 0.0004502923711386279, 0.000456923269229902, 0.000451463358571992, 0.0004492347779148642, 0.000456923269229902, 0.0004552793517524856, 0.0004618794922643704, 0.0004642047318755908, 0.0004624892566288283]
        ],
       "unconstrained":0.00693611750822962
      },
     "PP563828_1_2023_09_04":{
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":1e-06,
       "Posterior prob omega class":null,
       "original name":"PP563828_1_2023_09_04",
       "unconstrained":0
      },
     "PP563831_1_2023_08_29":{
       "MG94xREV with separate rates for branch sets":0.00330920730006597,
       "Nucleotide GTR":0.0033386370737857,
       "Posterior prob omega class":null,
       "original name":"PP563831_1_2023_08_29",
       "unconstrained":0.003302253315085909
      },
     "PP563832_1_2023_08_28":{
       "MG94xREV with separate rates for branch sets":0.003307231818943022,
       "Nucleotide GTR":0.003341256955363836,
       "Posterior prob omega class":null,
       "original name":"PP563832_1_2023_08_28",
       "unconstrained":0.003303419459318604
      },
     "PP563838_1_2023_09_30":{
       "MG94xREV with separate rates for branch sets":0.003319002112237459,
       "Nucleotide GTR":0.003338636346485376,
       "Posterior prob omega class":null,
       "original name":"PP563838_1_2023_09_30",
       "unconstrained":0.00331509905135317
      },
     "PP563839_1_2023_09_29":{
       "MG94xREV with separate rates for branch sets":0,
       "Nucleotide GTR":1e-06,
       "Posterior prob omega class":null,
       "original name":"PP563839_1_2023_09_29",
       "unconstrained":0
      },
     "PP563845_1_2023_10_22":{
       "MG94xREV with separate rates for branch sets":0.0058845576394677,
       "Nucleotide GTR":0.007154900994762849,
       "Posterior prob omega class":null,
       "original name":"PP563845_1_2023_10_22",
       "unconstrained":0.004619675953414121
      },
     "PP563880_1_2023_10_05":{
       "MG94xREV with separate rates for branch sets":0.003314849953190457,
       "Nucleotide GTR":0.003342118030716714,
       "Posterior prob omega class":null,
       "original name":"PP563880_1_2023_10_05",
       "unconstrained":0.003314120906029948
      },
     "PP563884_1_2023_09_24":{
       "MG94xREV with separate rates for branch sets":0.003311549872476787,
       "Nucleotide GTR":0.003341256955567041,
       "Posterior prob omega class":null,
       "original name":"PP563884_1_2023_09_24",
       "unconstrained":0.003307145870967826
      },
     "PP564823_1_2023_10_06":{
       "MG94xREV with separate rates for branch sets":0.04444969258775296,
       "Nucleotide GTR":0.04196108121510467,
       "Posterior prob omega class":null,
       "original name":"PP564823_1_2023_10_06",
       "unconstrained":0.04804177564386494
      }
    },
   "attributes":{
     "MG94xREV with separate rates for branch sets":{
       "attribute type":"branch length",
       "display order":1
      },
     "Nucleotide GTR":{
       "attribute type":"branch length",
       "display order":0
      },
     "Posterior prob omega class":{
       "attribute type":"branch annotations",
       "display order":4
      },
     "Posterior prob omega class by site":{
       "attribute type":"branch annotations",
       "display order":5
      },
     "original name":{
       "attribute type":"node label",
       "display order":0
      },
     "unconstrained":{
       "attribute type":"branch length",
       "display order":0
      }
    }
  },
 "data partitions":{
   "0":{
     "coverage":      [
[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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
      ],
     "name":"busted.filter.default"
    }
  },
 "fits":{
   "MG94xREV with separate rates for branch sets":{
     "AIC-c":1127.910850580984,
     "Equilibrium frequencies":      [
[0.04024763514913952],
      [0.01922996663172304],
      [0.03420070900547616],
      [0.014368896284083],
      [0.03368306905822573],
      [0.01609347460151461],
      [0.02862242313127222],
      [0.01202526618107644],
      [0.03424262136543949],
      [0.01636082378008254],
      [0.02909790661151763],
      [0.01222503317454278],
      [0.04878002735358049],
      [0.02330666869812213],
      [0.04145116886040549],
      [0.01741506429336918],
      [0.01835841860430346],
      [0.008771491191067078],
      [0.0156001944004883],
      [0.006554179193076294],
      [0.01536407988586604],
      [0.007340822446772941],
      [0.01305573416590236],
      [0.0054851637757677],
      [0.0156193121609741],
      [0.007462770186447074],
      [0.01327261957388795],
      [0.005576284808737427],
      [0.02225035479396483],
      [0.01063102412468302],
      [0.01890739435390807],
      [0.007943647847477694],
      [0.02003764925766833],
      [0.009573812850750063],
      [0.01702713237376286],
      [0.007153685002693248],
      [0.01676942064321455],
      [0.008012281919357385],
      [0.01424993228754379],
      [0.005986887554352669],
      [0.01704799882132915],
      [0.008145384126471394],
      [0.01448665603962682],
      [0.006086343359234239],
      [0.02428557790460417],
      [0.01160343585423386],
      [0.0206368394035431],
      [0.008670247303157035],
      [0.01086675715317312],
      [0.008119790817560615],
      [0.01903413243710357],
      [0.009094341326464849],
      [0.01617438694822276],
      [0.006795417266946891],
      [0.009245418998841326],
      [0.01644308026470771],
      [0.006908304587387538],
      [0.02756534742509875],
      [0.0131704809291841],
      [0.02342384645525713],
      [0.009841164995614077]
      ],
     "Log Likelihood":-535.0231635224093,
     "Rate Distributions":{
       "non-synonymous/synonymous rate ratio for *background*":        [
[0.2332468645873907, 1]
        ],
       "non-synonymous/synonymous rate ratio for *test*":        [
[0.05436826671559885, 1]
        ]
      },
     "display order":1,
     "estimated parameters":28
    },
   "Nucleotide GTR":{
     "AIC-c":1165.694393932368,
     "Equilibrium frequencies":      [
[0.3348148148148147],
      [0.202962962962963],
      [0.2462962962962963],
      [0.2159259259259259]
      ],
     "Log Likelihood":-559.6409189392783,
     "Rate Distributions":{
       "Substitution rate from nucleotide A to nucleotide C":0.1057602468701381,
       "Substitution rate from nucleotide A to nucleotide G":1,
       "Substitution rate from nucleotide A to nucleotide T":0,
       "Substitution rate from nucleotide C to nucleotide G":0.1465960735122673,
       "Substitution rate from nucleotide C to nucleotide T":2.269319946484975,
       "Substitution rate from nucleotide G to nucleotide T":0.1391184331291334
      },
     "display order":0,
     "estimated parameters":23
    },
   "Unconstrained model":{
     "AIC-c":1164.066233233619,
     "Log Likelihood":-534.6092290289872,
     "Rate Distributions":{
       "Background":{
         "0":{
           "omega":236.9358471479831,
           "proportion":0
          },
         "1":{
           "omega":0.2100294329667581,
           "proportion":0.5542688958966767
          },
         "2":{
           "omega":0.255710153738319,
           "proportion":0.4457311041033233
          },
         "3":{
           "omega":0.2978621753285197,
           "proportion":0
          }
        },
       "Synonymous site-to-site rates":{
         "0":{
           "proportion":0.3409863833415702,
           "rate":0
          },
         "1":{
           "proportion":0.6590136166584298,
           "rate":1.517419329012598
          },
         "2":{
           "proportion":0,
           "rate":1.52677760828329
          }
        },
       "Test":{
         "0":{
           "omega":226.0589415365084,
           "proportion":0
          },
         "1":{
           "omega":0.04198616898833647,
           "proportion":0.9147510556650086
          },
         "2":{
           "omega":0.1430120656070995,
           "proportion":0.08477641331245425
          },
         "3":{
           "omega":1,
           "proportion":0.0004725310225371633
          }
        }
      },
     "display order":2,
     "estimated parameters":45
    }
  },
 "input":{
   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/87/f4fe290e4b23b20d10420f0110f410/capsid_protein_C-nodups.fasta",
   "number of sequences":9,
   "number of sites":100,
   "partition count":1,
   "trees":{
     "0":"(PP563828_1_2023_09_04,PP563831_1_2023_08_29,PP563880_1_2023_10_05,((PP564823_1_2023_10_06,PP563845_1_2023_10_22)Node4,(PP563884_1_2023_09_24,PP563838_1_2023_09_30,PP563839_1_2023_09_29)Node7)Node3,PP563832_1_2023_08_28)"
    }
  },
 "runtime":"2.5.73",
 "substitutions":{
   "0":{
     "0":{
       "root":"ATG"
      },
     "1":{
       "root":"AAC"
      },
     "10":{
       "root":"CCG"
      },
     "11":{
       "root":"TCT"
      },
     "12":{
       "root":"TTC"
      },
     "13":{
       "root":"AAT"
      },
     "14":{
       "root":"ATG"
      },
     "15":{
       "root":"CTG"
      },
     "16":{
       "root":"AAA"
      },
     "17":{
       "root":"CGC"
      },
     "18":{
       "root":"GCG"
      },
     "19":{
       "root":"AGA"
      },
     "2":{
       "root":"AAC"
      },
     "20":{
       "root":"AAC"
      },
     "21":{
       "root":"CGC"
      },
     "22":{
       "root":"GTG"
      },
     "23":{
       "root":"TCA"
      },
     "24":{
       "root":"ACT"
      },
     "25":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GTT"
      },
     "26":{
       "Node7":"TCA",
       "PP564823_1_2023_10_06":"TCA",
       "root":"CCA"
      },
     "27":{
       "root":"CAG"
      },
     "28":{
       "root":"TTG"
      },
     "29":{
       "root":"GCG"
      },
     "3":{
       "root":"CAA"
      },
     "30":{
       "root":"AAG"
      },
     "31":{
       "root":"AGA"
      },
     "32":{
       "root":"TTC"
      },
     "33":{
       "root":"TCA"
      },
     "34":{
       "PP563831_1_2023_08_29":"GAA",
       "root":"AAA"
      },
     "35":{
       "root":"GGA"
      },
     "36":{
       "root":"TTG"
      },
     "37":{
       "Node7":"CTT",
       "root":"CTC"
      },
     "38":{
       "PP563884_1_2023_09_24":"TTA",
       "root":"TCA"
      },
     "39":{
       "root":"GGC"
      },
     "4":{
       "PP563845_1_2023_10_22":"CGA",
       "root":"CGG"
      },
     "40":{
       "Node4":"CAA",
       "root":"CAG"
      },
     "41":{
       "root":"GGA"
      },
     "42":{
       "root":"CCC"
      },
     "43":{
       "root":"ATG"
      },
     "44":{
       "root":"AAA"
      },
     "45":{
       "PP563880_1_2023_10_05":"CTA",
       "PP564823_1_2023_10_06":"ATG",
       "root":"CTG"
      },
     "46":{
       "root":"GTG"
      },
     "47":{
       "root":"ATG"
      },
     "48":{
       "root":"GCT"
      },
     "49":{
       "Node3":"TTC",
       "root":"TTT"
      },
     "5":{
       "PP564823_1_2023_10_06":"AAG",
       "root":"AAA"
      },
     "50":{
       "root":"ATA"
      },
     "51":{
       "root":"GCA"
      },
     "52":{
       "root":"TTC"
      },
     "53":{
       "root":"CTA"
      },
     "54":{
       "root":"AGA"
      },
     "55":{
       "Node4":"TTT",
       "root":"TTC"
      },
     "56":{
       "root":"CTA"
      },
     "57":{
       "root":"GCC"
      },
     "58":{
       "root":"ATA"
      },
     "59":{
       "Node3":"CCC",
       "root":"CCT"
      },
     "6":{
       "root":"AAG"
      },
     "60":{
       "root":"CCA"
      },
     "61":{
       "root":"ACA"
      },
     "62":{
       "root":"GCA"
      },
     "63":{
       "Node4":"GGA",
       "root":"GGG"
      },
     "64":{
       "root":"ATT"
      },
     "65":{
       "root":"TTG"
      },
     "66":{
       "root":"GCT"
      },
     "67":{
       "root":"AGA"
      },
     "68":{
       "root":"TGG"
      },
     "69":{
       "Node4":"GGC",
       "PP564823_1_2023_10_06":"AGC",
       "root":"GGT"
      },
     "7":{
       "root":"ACG"
      },
     "70":{
       "root":"TCA"
      },
     "71":{
       "root":"TTC"
      },
     "72":{
       "root":"AAG"
      },
     "73":{
       "root":"AAG"
      },
     "74":{
       "root":"AAT"
      },
     "75":{
       "root":"GGA"
      },
     "76":{
       "root":"GCG"
      },
     "77":{
       "root":"ATC"
      },
     "78":{
       "root":"AAA"
      },
     "79":{
       "root":"GTG"
      },
     "8":{
       "PP564823_1_2023_10_06":"GGT",
       "root":"GCT"
      },
     "80":{
       "PP563838_1_2023_09_30":"CTG",
       "PP564823_1_2023_10_06":"TTA",
       "root":"CTA"
      },
     "81":{
       "root":"CGG"
      },
     "82":{
       "root":"GGT"
      },
     "83":{
       "PP563832_1_2023_08_28":"TTT",
       "root":"TTC"
      },
     "84":{
       "PP564823_1_2023_10_06":"AAA",
       "root":"AAG"
      },
     "85":{
       "root":"AAA"
      },
     "86":{
       "PP564823_1_2023_10_06":"GAG",
       "root":"GAA"
      },
     "87":{
       "root":"ATC"
      },
     "88":{
       "root":"TCA"
      },
     "89":{
       "root":"AGC"
      },
     "9":{
       "root":"CGA"
      },
     "90":{
       "root":"ATG"
      },
     "91":{
       "PP563845_1_2023_10_22":"TTG",
       "root":"CTG"
      },
     "92":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
      },
     "93":{
       "root":"ATA"
      },
     "94":{
       "root":"ATG"
      },
     "95":{
       "PP564823_1_2023_10_06":"AAC",
       "root":"AAT"
      },
     "96":{
       "PP564823_1_2023_10_06":"AGG",
       "root":"AGA"
      },
     "97":{
       "root":"AGG"
      },
     "98":{
       "root":"AAA"
      },
     "99":{
       "root":"AGA"
      }
    }
  },
 "test results":{
   "LRT":0,
   "p-value":0.5
  },
 "tested":{
   "0":{
     "Node3":"test",
     "Node4":"test",
     "Node7":"test",
     "PP563828_1_2023_09_04":"background",
     "PP563831_1_2023_08_29":"background",
     "PP563832_1_2023_08_28":"background",
     "PP563838_1_2023_09_30":"background",
     "PP563839_1_2023_09_29":"background",
     "PP563845_1_2023_10_22":"background",
     "PP563880_1_2023_10_05":"background",
     "PP563884_1_2023_09_24":"background",
     "PP564823_1_2023_10_06":"background"
    }
  },
 "timers":{
   "Overall":{
     "order":0,
     "timer":28
    },
   "Preliminary model fitting":{
     "order":1,
     "timer":2
    },
   "Unconstrained BUSTED model fitting":{
     "order":2,
     "timer":25
    }
  }
}