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_id	taxon_name	nb_trans	nb_canon_trans	nb_trans_spectree	nb_trans_anctree	nb_trans_orphan	perc_trans_spectree	perc_trans_anctree	perc_trans_orphan
7757	Petromyzon marinus	2628	2628	0	68	2560	0.00	2.59	97.41
7897	Latimeria chalumnae	2918	2918	0	367	2551	0.00	12.58	87.42
28377	Anolis carolinensis	3160	3160	6	821	2333	0.19	25.98	73.83
9103	Meleagris gallopavo	756	756	0	410	346	0.00	54.23	45.77
9031	Gallus gallus	1102	1102	0	242	860	0.00	21.96	78.04
59729	Taeniopygia guttata	724	724	0	467	257	0.00	64.50	35.50
9258	Ornithorhynchus anatinus	3871	3871	0	556	3315	0.00	14.36	85.64
9361	Dasypus novemcinctus	4475	4475	0	102	4373	0.00	2.28	97.72
9358	Choloepus hoffmanni	2030	2030	0	72	1958	0.00	3.55	96.45
37347	Tupaia belangeri	3049	3049	0	234	2815	0.00	7.67	92.33
10020	Dipodomys ordii	3036	3036	0	135	2901	0.00	4.45	95.55
10090	Mus musculus	8538	7543	0	2619	4924	0.00	34.72	65.28
10116	Rattus norvegicus	4828	4828	0	1456	3372	0.00	30.16	69.84
43179	Ictidomys tridecemlineatus	3166	3166	0	670	2496	0.00	21.16	78.84
10141	Cavia porcellus	5963	5963	0	170	5793	0.00	2.85	97.15
9978	Ochotona princeps	5708	5708	0	111	5597	0.00	1.94	98.06
9986	Oryctolagus cuniculus	3375	3375	0	155	3220	0.00	4.59	95.41
9478	Tarsius syrichta	5362	5362	0	109	5253	0.00	2.03	97.97
9544	Macaca mulatta	6579	6579	0	2625	3954	0.00	39.90	60.10
9601	Pongo abelii	6996	6996	0	2825	4171	0.00	40.38	59.62
9598	Pan troglodytes	8657	8657	0	5262	3395	0.00	60.78	39.22
9606	Homo sapiens	18406	14652	6	4223	10423	0.04	28.82	71.14
9593	Gorilla gorilla	6701	6701	0	2763	3938	0.00	41.23	58.77
61853	Nomascus leucogenys	7172	7172	0	386	6786	0.00	5.38	94.62
9483	Callithrix jacchus	9000	9000	0	5842	3158	0.00	64.91	35.09
30611	Otolemur garnettii	7276	7276	0	182	7094	0.00	2.50	97.50
30608	Microcebus murinus	7111	7111	0	153	6958	0.00	2.15	97.85
132908	Pteropus vampyrus	4171	4171	0	309	3862	0.00	7.41	92.59
59463	Myotis lucifugus	4408	4408	0	329	4079	0.00	7.46	92.54
9685	Felis catus	2930	2930	0	122	2808	0.00	4.16	95.84
9646	Ailuropoda melanoleuca	3141	3141	0	183	2958	0.00	5.83	94.17
9615	Canis familiaris	3613	3613	0	1101	2512	0.00	30.47	69.53
9796	Equus caballus	2118	2118	0	804	1314	0.00	37.96	62.04
42254	Sorex araneus	4558	4558	0	83	4475	0.00	1.82	98.18
9365	Erinaceus europaeus	6432	6432	0	101	6331	0.00	1.57	98.43
30538	Vicugna pacos	2508	2508	0	96	2412	0.00	3.83	96.17
9823	Sus scrofa	2989	2989	0	1412	1577	0.00	47.24	52.76
9913	Bos taurus	3825	3825	0	811	3014	0.00	21.20	78.80
9739	Tursiops truncatus	3766	3766	0	168	3598	0.00	4.46	95.54
9785	Loxodonta africana	2644	2644	0	341	2303	0.00	12.90	87.10
9813	Procavia capensis	1696	1696	0	239	1457	0.00	14.09	85.91
9371	Echinops telfairi	5656	5656	0	109	5547	0.00	1.93	98.07
13616	Monodelphis domestica	1850	1850	0	517	1333	0.00	27.95	72.05
9305	Sarcophilus harrisii	1490	1490	0	709	781	0.00	47.58	52.42
9315	Macropus eugenii	1472	1472	0	597	875	0.00	40.56	59.44
8364	Xenopus tropicalis	1282	1282	0	474	808	0.00	36.97	63.03
99883	Tetraodon nigroviridis	813	813	0	354	459	0.00	43.54	56.46
31033	Takifugu rubripes	703	703	0	325	378	0.00	46.23	53.77
69293	Gasterosteus aculeatus	1617	1617	0	604	1013	0.00	37.35	62.65
8090	Oryzias latipes	735	735	0	296	439	0.00	40.27	59.73
8128	Oreochromis niloticus	821	821	0	487	334	0.00	59.32	40.68
8049	Gadus morhua	1541	1541	0	371	1170	0.00	24.08	75.92
7955	Danio rerio	4598	4556	0	1264	3292	0.00	27.74	72.26
7719	Ciona intestinalis	455	455	0	34	421	0.00	7.47	92.53
51511	Ciona savignyi	314	314	0	118	196	0.00	37.58	62.42
7227	Drosophila melanogaster	1031	970	NULL	0	NULL	NULL	0.00	NULL
6239	Caenorhabditis elegans	23655	23650	NULL	0	NULL	NULL	0.00	NULL
4932	Saccharomyces cerevisiae	413	413	NULL	0	NULL	NULL	0.00	NULL
	Total	239832	234975	12	45383	189580	0.01	19.31	80.68

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

taxon_id	taxon_name	nb_trees	tot_nb_trans	avg_nb_trans	max_nb_trans	avg_nb_spec	max_nb_spec	avg_nb_trans_per_spec
7711	Chordata	30	13594	453.13	3828	41.47	54	12.76
7742	Vertebrata	33	3770	114.24	753	42.79	53	2.69
117571	Euteleostomi	176	17335	98.49	5412	18.35	51	5.90
8287	Sarcopterygii	7	217	31.00	43	28.57	42	1.15
32523	Tetrapoda	6	328	54.67	147	36.33	40	1.46
32524	Amniota	61	1240	20.33	93	11.15	40	1.93
28377	Anolis carolinensis	1	6	6.00	6	1.00	1	6.00
40674	Mammalia	10	345	34.50	112	25.50	39	1.25
32525	Theria	23	2948	128.17	2285	10.65	29	15.00
9347	Eutheria	156	5606	35.94	750	14.30	35	2.76
9606	Homo sapiens	1	6	6.00	6	1.00	1	6.00
	Total	504	45395	90.07	5412	19.28	54	4.85

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

taxon_id	taxon_name	nb_nodes	nb_spec_nodes	nb_dup_nodes	nb_dubious_nodes	avg_dupscore	avg_dupscore_nondub
7711	Chordata	139	34	95	10	0.38	0.38
7742	Vertebrata	136	64	69	3	0.34	0.34
7757	Petromyzon marinus	2	0	2	0	1.00	1.00
117571	Euteleostomi	1969	528	1109	332	0.23	0.23
8287	Sarcopterygii	588	230	270	88	0.35	0.35
7897	Latimeria chalumnae	70	0	70	0	1.00	1.00
32523	Tetrapoda	349	166	105	78	0.32	0.32
32524	Amniota	1527	602	624	301	0.31	0.31
32561	Sauria	740	710	30	0	0.66	0.66
28377	Anolis carolinensis	269	0	269	0	1.00	1.00
9103	Meleagris gallopavo	11	0	11	0	1.00	1.00
9031	Gallus gallus	12	0	12	0	1.00	1.00
59729	Taeniopygia guttata	80	0	80	0	1.00	1.00
40674	Mammalia	455	225	126	104	0.30	0.30
9258	Ornithorhynchus anatinus	200	0	200	0	1.00	1.00
32525	Theria	1278	539	562	177	0.37	0.37
9347	Eutheria	28982	22258	6724	0	0.55	0.55
37347	Tupaia belangeri	10	0	10	0	1.00	1.00
10020	Dipodomys ordii	2	0	2	0	1.00	1.00
10090	Mus musculus	1152	0	1152	0	1.00	1.00
10116	Rattus norvegicus	166	0	166	0	1.00	1.00
43179	Ictidomys tridecemlineatus	20	0	20	0	1.00	1.00
10141	Cavia porcellus	2	0	2	0	1.00	1.00
9978	Ochotona princeps	1	0	1	0	1.00	1.00
9478	Tarsius syrichta	1	0	1	0	1.00	1.00
9544	Macaca mulatta	123	0	123	0	1.00	1.00
9601	Pongo abelii	187	0	187	0	1.00	1.00
9598	Pan troglodytes	451	0	451	0	1.00	1.00
9606	Homo sapiens	78	0	78	0	1.00	1.00
9593	Gorilla gorilla	105	0	105	0	1.00	1.00
61853	Nomascus leucogenys	2	0	2	0	1.00	1.00
9483	Callithrix jacchus	1157	0	1157	0	1.00	1.00
30608	Microcebus murinus	1	0	1	0	1.00	1.00
132908	Pteropus vampyrus	7	0	7	0	1.00	1.00
59463	Myotis lucifugus	20	0	20	0	1.00	1.00
9615	Canis familiaris	84	0	84	0	1.00	1.00
9796	Equus caballus	34	0	34	0	1.00	1.00
42254	Sorex araneus	1	0	1	0	1.00	1.00
9365	Erinaceus europaeus	1	0	1	0	1.00	1.00
30538	Vicugna pacos	1	0	1	0	1.00	1.00
9823	Sus scrofa	289	0	289	0	1.00	1.00
9913	Bos taurus	39	0	39	0	1.00	1.00
9785	Loxodonta africana	20	0	20	0	1.00	1.00
9813	Procavia capensis	4	0	4	0	1.00	1.00
9263	Marsupialia	705	615	90	0	0.61	0.61
13616	Monodelphis domestica	60	0	60	0	1.00	1.00
9305	Sarcophilus harrisii	73	0	73	0	1.00	1.00
9315	Macropus eugenii	36	0	36	0	1.00	1.00
8364	Xenopus tropicalis	242	0	242	0	1.00	1.00
186625	Clupeocephala	1502	1342	160	0	0.51	0.51
99883	Tetraodon nigroviridis	94	0	94	0	1.00	1.00
31033	Takifugu rubripes	48	0	48	0	1.00	1.00
69293	Gasterosteus aculeatus	212	0	212	0	1.00	1.00
8090	Oryzias latipes	35	0	35	0	1.00	1.00
8128	Oreochromis niloticus	57	0	57	0	1.00	1.00
8049	Gadus morhua	110	0	110	0	1.00	1.00
7955	Danio rerio	835	0	835	0	1.00	1.00
7718	Ciona	55	27	28	0	0.59	0.59
7719	Ciona intestinalis	3	0	3	0	1.00	1.00
51511	Ciona savignyi	59	0	59	0	1.00	1.00
	Total (ancestral species)	38425	27340	9992	1093	0.48	0.48
	Total (extant species)	6466	0	6466	0	1.00	1.00
	Total	44891	27340	16458	1093	0.68	0.68