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Statistics on ncRNA trees

ncRNA trees

Since release 58, Compara computes phylogenetic trees for the non-coding RNAs annotating by RFAM. The manuscript is in preparation. More information can be obtained here

  • Gene coverage: Number of genes and members in total, included in trees (either species-specific, or encompassing other species), and orphaned (not in any tree)
  • Tree size: Sizes of trees (genes, and distinct species), grouped according to the root ancestral species
  • Predicted gene events: For each ancestral species, number of speciation and duplication nodes (inc. dubious ones), with the average duplication score

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Number of genes and members in total, included in trees (either species-specific, or encompassing other species), and orphaned (not in any tree)

taxon_idtaxon_namenb_transnb_canon_transnb_trans_spectreenb_trans_anctreenb_trans_orphanperc_trans_spectreeperc_trans_anctreeperc_trans_orphan
7757Petromyzon marinus2628262806825600.002.5997.41
7897Latimeria chalumnae29182918036725510.0012.5887.42
28377Anolis carolinensis31603160682123330.1925.9873.83
9103Meleagris gallopavo75675604103460.0054.2345.77
9031Gallus gallus1102110202428600.0021.9678.04
59729Taeniopygia guttata72472404672570.0064.5035.50
9258Ornithorhynchus anatinus38713871055633150.0014.3685.64
9361Dasypus novemcinctus44754475010243730.002.2897.72
9358Choloepus hoffmanni2030203007219580.003.5596.45
37347Tupaia belangeri30493049023428150.007.6792.33
10020Dipodomys ordii30363036013529010.004.4595.55
10090Mus musculus853875430261949240.0034.7265.28
10116Rattus norvegicus482848280145633720.0030.1669.84
43179Ictidomys tridecemlineatus31663166067024960.0021.1678.84
10141Cavia porcellus59635963017057930.002.8597.15
9978Ochotona princeps57085708011155970.001.9498.06
9986Oryctolagus cuniculus33753375015532200.004.5995.41
9478Tarsius syrichta53625362010952530.002.0397.97
9544Macaca mulatta657965790262539540.0039.9060.10
9601Pongo abelii699669960282541710.0040.3859.62
9598Pan troglodytes865786570526233950.0060.7839.22
9606Homo sapiens184061465264223104230.0428.8271.14
9593Gorilla gorilla670167010276339380.0041.2358.77
61853Nomascus leucogenys71727172038667860.005.3894.62
9483Callithrix jacchus900090000584231580.0064.9135.09
30611Otolemur garnettii72767276018270940.002.5097.50
30608Microcebus murinus71117111015369580.002.1597.85
132908Pteropus vampyrus41714171030938620.007.4192.59
59463Myotis lucifugus44084408032940790.007.4692.54
9685Felis catus29302930012228080.004.1695.84
9646Ailuropoda melanoleuca31413141018329580.005.8394.17
9615Canis familiaris361336130110125120.0030.4769.53
9796Equus caballus21182118080413140.0037.9662.04
42254Sorex araneus4558455808344750.001.8298.18
9365Erinaceus europaeus64326432010163310.001.5798.43
30538Vicugna pacos2508250809624120.003.8396.17
9823Sus scrofa298929890141215770.0047.2452.76
9913Bos taurus38253825081130140.0021.2078.80
9739Tursiops truncatus37663766016835980.004.4695.54
9785Loxodonta africana26442644034123030.0012.9087.10
9813Procavia capensis16961696023914570.0014.0985.91
9371Echinops telfairi56565656010955470.001.9398.07
13616Monodelphis domestica18501850051713330.0027.9572.05
9305Sarcophilus harrisii1490149007097810.0047.5852.42
9315Macropus eugenii1472147205978750.0040.5659.44
8364Xenopus tropicalis1282128204748080.0036.9763.03
99883Tetraodon nigroviridis81381303544590.0043.5456.46
31033Takifugu rubripes70370303253780.0046.2353.77
69293Gasterosteus aculeatus16171617060410130.0037.3562.65
8090Oryzias latipes73573502964390.0040.2759.73
8128Oreochromis niloticus82182104873340.0059.3240.68
8049Gadus morhua15411541037111700.0024.0875.92
7955Danio rerio459845560126432920.0027.7472.26
7719Ciona intestinalis4554550344210.007.4792.53
51511Ciona savignyi31431401181960.0037.5862.42
7227Drosophila melanogaster1031970NULL0NULLNULL0.00NULL
6239Caenorhabditis elegans2365523650NULL0NULLNULL0.00NULL
4932Saccharomyces cerevisiae413413NULL0NULLNULL0.00NULL
Total23983223497512453831895800.0119.3180.68

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Sizes of trees (genes, and distinct species), grouped according to the root ancestral species

taxon_idtaxon_namenb_treestot_nb_transavg_nb_transmax_nb_transavg_nb_specmax_nb_specavg_nb_trans_per_spec
7711Chordata3013594453.13382841.475412.76
7742Vertebrata333770114.2475342.79532.69
117571Euteleostomi1761733598.49541218.35515.90
8287Sarcopterygii721731.004328.57421.15
32523Tetrapoda632854.6714736.33401.46
32524Amniota61124020.339311.15401.93
28377Anolis carolinensis166.0061.0016.00
40674Mammalia1034534.5011225.50391.25
32525Theria232948128.17228510.652915.00
9347Eutheria156560635.9475014.30352.76
9606Homo sapiens166.0061.0016.00
Total5044539590.07541219.28544.85

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For each ancestral species, number of speciation and duplication nodes (inc. dubious ones), with the average duplication score

taxon_idtaxon_namenb_nodesnb_spec_nodesnb_dup_nodesnb_dubious_nodesnb_gene_splitsavg_dupscoreavg_dupscore_nondub
7711Chordata13934951000.380.38
7742Vertebrata1366469300.340.34
7757Petromyzon marinus202001.001.00
117571Euteleostomi1969528110933200.230.23
8287Sarcopterygii5882302708800.350.35
7897Latimeria chalumnae70070001.001.00
32523Tetrapoda3491661057800.320.32
32524Amniota152760262430100.310.31
32561Sauria74071030000.660.66
28377Anolis carolinensis2690269001.001.00
9103Meleagris gallopavo11011001.001.00
9031Gallus gallus12012001.001.00
59729Taeniopygia guttata80080001.001.00
40674Mammalia45522512610400.300.30
9258Ornithorhynchus anatinus2000200001.001.00
32525Theria127853956217700.370.37
9347Eutheria28982222586724000.550.55
37347Tupaia belangeri10010001.001.00
10020Dipodomys ordii202001.001.00
10090Mus musculus115201152001.001.00
10116Rattus norvegicus1660166001.001.00
43179Ictidomys tridecemlineatus20020001.001.00
10141Cavia porcellus202001.001.00
9978Ochotona princeps101001.001.00
9478Tarsius syrichta101001.001.00
9544Macaca mulatta1230123001.001.00
9601Pongo abelii1870187001.001.00
9598Pan troglodytes4510451001.001.00
9606Homo sapiens78078001.001.00
9593Gorilla gorilla1050105001.001.00
61853Nomascus leucogenys202001.001.00
9483Callithrix jacchus115701157001.001.00
30608Microcebus murinus101001.001.00
132908Pteropus vampyrus707001.001.00
59463Myotis lucifugus20020001.001.00
9615Canis familiaris84084001.001.00
9796Equus caballus34034001.001.00
42254Sorex araneus101001.001.00
9365Erinaceus europaeus101001.001.00
30538Vicugna pacos101001.001.00
9823Sus scrofa2890289001.001.00
9913Bos taurus39039001.001.00
9785Loxodonta africana20020001.001.00
9813Procavia capensis404001.001.00
9263Marsupialia70561590000.610.61
13616Monodelphis domestica60060001.001.00
9305Sarcophilus harrisii73073001.001.00
9315Macropus eugenii36036001.001.00
8364Xenopus tropicalis2420242001.001.00
186625Clupeocephala15021342160000.510.51
99883Tetraodon nigroviridis94094001.001.00
31033Takifugu rubripes48048001.001.00
69293Gasterosteus aculeatus2120212001.001.00
8090Oryzias latipes35035001.001.00
8128Oreochromis niloticus57057001.001.00
8049Gadus morhua1100110001.001.00
7955Danio rerio8350835001.001.00
7718Ciona552728000.590.59
7719Ciona intestinalis303001.001.00
51511Ciona savignyi59059001.001.00
Total (ancestral species)38425273409992109300.480.48
Total (extant species)646606466001.001.00
Total448912734016458109300.680.68