Statistics on protein trees

Protein trees

The protein tree pipeline is described at the following page.

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

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_pep	nb_canon_pep	nb_pep_spectree	nb_pep_anctree	nb_pep_orphan	perc_pep_spectree	perc_pep_anctree	perc_pep_orphan
7757	Petromyzon marinus	11429	10402	174	9899	329	1.67	95.16	3.16
7897	Latimeria chalumnae	23599	19567	429	18997	141	2.19	97.09	0.72
28377	Anolis carolinensis	18939	17792	135	17383	274	0.76	97.70	1.54
9103	Meleagris gallopavo	16483	14112	2	13962	148	0.01	98.94	1.05
9031	Gallus gallus	22194	16736	124	14994	1618	0.74	89.59	9.67
59729	Taeniopygia guttata	18204	17488	231	16919	338	1.32	96.75	1.93
9258	Ornithorhynchus anatinus	26836	17951	394	16882	675	2.19	94.04	3.76
9361	Dasypus novemcinctus	14846	14803	32	14607	164	0.22	98.68	1.11
9358	Choloepus hoffmanni	12435	12393	0	12289	104	0.00	99.16	0.84
37347	Tupaia belangeri	15462	15458	48	15221	189	0.31	98.47	1.22
10020	Dipodomys ordii	15853	15798	2	15661	135	0.01	99.13	0.85
10090	Mus musculus	56766	23075	259	21972	844	1.12	95.22	3.66
10116	Rattus norvegicus	32971	22938	49	22264	625	0.21	97.06	2.72
43179	Ictidomys tridecemlineatus	20000	18826	0	18785	41	0.00	99.78	0.22
10141	Cavia porcellus	19774	18673	7	18511	155	0.04	99.13	0.83
9978	Ochotona princeps	15993	15993	9	15796	188	0.06	98.77	1.18
9986	Oryctolagus cuniculus	23812	19018	6	18918	94	0.03	99.47	0.49
9478	Tarsius syrichta	13662	13615	17	13470	128	0.12	98.93	0.94
9544	Macaca mulatta	36384	21905	97	21445	363	0.44	97.90	1.66
9601	Pongo abelii	23533	20068	50	19551	467	0.25	97.42	2.33
9598	Pan troglodytes	19894	18746	4	18619	123	0.02	99.32	0.66
9606	Homo sapiens	93072	20479	7	20199	273	0.03	98.63	1.33
9593	Gorilla gorilla	27473	20962	43	20477	442	0.21	97.69	2.11
61853	Nomascus leucogenys	23186	18161	0	18061	100	0.00	99.45	0.55
9483	Callithrix jacchus	43792	20993	8	20769	216	0.04	98.93	1.03
30611	Otolemur garnettii	19986	19506	0	19438	68	0.00	99.65	0.35
30608	Microcebus murinus	16319	16319	10	16153	156	0.06	98.98	0.96
132908	Pteropus vampyrus	17053	16990	2	16891	97	0.01	99.42	0.57
59463	Myotis lucifugus	20719	19728	8	19579	141	0.04	99.24	0.71
9685	Felis catus	15048	15048	2	14873	173	0.01	98.84	1.15
9646	Ailuropoda melanoleuca	21136	19343	0	19191	152	0.00	99.21	0.79
9615	Canis familiaris	25559	19305	10	19146	149	0.05	99.18	0.77
9796	Equus caballus	22641	20436	723	19513	200	3.54	95.48	0.98
42254	Sorex araneus	13192	13187	14	13007	166	0.11	98.64	1.26
9365	Erinaceus europaeus	14592	14588	8	14426	154	0.05	98.89	1.06
30538	Vicugna pacos	11793	11752	10	11666	76	0.09	99.27	0.65
9823	Sus scrofa	23118	21640	35	21251	354	0.16	98.20	1.64
9913	Bos taurus	22118	19994	31	19870	93	0.16	99.38	0.47
9739	Tursiops truncatus	16598	16537	2	16452	83	0.01	99.49	0.50
9785	Loxodonta africana	25635	20033	23	19917	93	0.11	99.42	0.46
9813	Procavia capensis	16101	16044	2	15886	156	0.01	99.02	0.97
9371	Echinops telfairi	16562	16562	93	16161	308	0.56	97.58	1.86
13616	Monodelphis domestica	32541	19466	74	19097	295	0.38	98.10	1.52
9305	Sarcophilus harrisii	22404	18788	119	18205	464	0.63	96.90	2.47
9315	Macropus eugenii	15342	15290	4	15205	81	0.03	99.44	0.53
8364	Xenopus tropicalis	22705	18429	469	17874	86	2.54	96.99	0.47
99883	Tetraodon nigroviridis	23118	19602	54	19238	310	0.28	98.14	1.58
31033	Takifugu rubripes	47841	18523	4	18440	79	0.02	99.55	0.43
69293	Gasterosteus aculeatus	27576	20787	111	19997	679	0.53	96.20	3.27
8090	Oryzias latipes	24661	19686	373	18529	784	1.89	94.12	3.98
8128	Oreochromis niloticus	26763	21437	110	21201	126	0.51	98.90	0.59
8049	Gadus morhua	22100	20095	108	19662	325	0.54	97.85	1.62
7955	Danio rerio	42159	26206	816	24873	517	3.11	94.91	1.97
7719	Ciona intestinalis	17302	16671	457	11875	4339	2.74	71.23	26.03
51511	Ciona savignyi	20143	11604	220	9963	1421	1.90	85.86	12.25
7227	Drosophila melanogaster	23849	13917	1983	9182	2752	14.25	65.98	19.77
6239	Caenorhabditis elegans	31234	20517	6862	8721	4934	33.45	42.51	24.05
4932	Saccharomyces cerevisiae	6692	6692	1143	2864	2685	17.08	42.80	40.12
	Total	1371192	1030674	16007	983997	30670	1.55	95.47	2.98

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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_pep	avg_nb_pep	max_nb_pep	avg_nb_spec	max_nb_spec	avg_nb_pep_per_spec
33154	Opisthokonta	2330	244603	104.98	400	51.41	58	2.00
33213	Bilateria	2370	298866	126.10	400	49.04	57	2.48
33316	Coelomata	1062	96144	90.53	400	45.03	56	1.95
7711	Chordata	1231	91146	74.04	398	37.58	55	1.84
7742	Vertebrata	784	68783	87.73	399	36.36	53	2.14
7757	Petromyzon marinus	49	174	3.55	14	1.00	1	3.55
117571	Euteleostomi	1568	81707	52.11	396	29.17	52	1.86
8287	Sarcopterygii	284	9985	35.16	395	20.56	45	1.87
7897	Latimeria chalumnae	48	429	8.94	37	1.00	1	8.94
32523	Tetrapoda	152	11903	78.31	395	23.74	44	3.29
32524	Amniota	454	15821	34.85	393	17.32	43	1.70
32561	Sauria	16	46	2.88	4	2.63	4	1.13
28377	Anolis carolinensis	22	135	6.14	24	1.00	1	6.14
8825	Neognathae	328	1247	3.80	297	2.09	3	1.58
9005	Phasianidae	15	92	6.13	31	2.00	2	3.07
9103	Meleagris gallopavo	1	2	2.00	2	1.00	1	2.00
9031	Gallus gallus	32	124	3.88	15	1.00	1	3.88
59729	Taeniopygia guttata	43	231	5.37	17	1.00	1	5.37
40674	Mammalia	295	16253	55.09	399	17.61	39	2.25
9258	Ornithorhynchus anatinus	53	394	7.43	27	1.00	1	7.43
32525	Theria	399	15106	37.86	398	18.31	38	1.74
9347	Eutheria	1201	17436	14.52	323	9.21	35	1.32
9348	Xenarthra	5	10	2.00	2	2.00	2	1.00
9361	Dasypus novemcinctus	7	32	4.57	14	1.00	1	4.57
314146	Euarchontoglires	127	857	6.75	321	3.66	18	1.36
37347	Tupaia belangeri	13	48	3.69	11	1.00	1	3.69
314147	Glires	9	28	3.11	7	2.00	2	1.56
9989	Rodentia	3	7	2.33	3	2.33	3	1.00
33553	Sciurognathi	15	50	3.33	14	2.47	3	1.29
10020	Dipodomys ordii	1	2	2.00	2	1.00	1	2.00
39107	Murinae	159	778	4.89	65	2.00	2	2.45
10090	Mus musculus	44	259	5.89	22	1.00	1	5.89
10116	Rattus norvegicus	13	49	3.77	16	1.00	1	3.77
10141	Cavia porcellus	3	7	2.33	3	1.00	1	2.33
9978	Ochotona princeps	3	9	3.00	4	1.00	1	3.00
9986	Oryctolagus cuniculus	2	6	3.00	4	1.00	1	3.00
9443	Primates	95	653	6.87	215	4.14	10	1.39
376913	Haplorrhini	18	76	4.22	9	4.00	7	1.07
9478	Tarsius syrichta	6	17	2.83	5	1.00	1	2.83
314293	Simiiformes	192	1340	6.98	162	3.69	7	1.55
9526	Catarrhini	135	560	4.15	29	2.80	6	1.46
9544	Macaca mulatta	35	97	2.77	10	1.00	1	2.77
314295	Hominoidea	212	709	3.34	20	3.10	5	1.07
9604	Hominidae	182	503	2.76	21	2.42	4	1.11
9601	Pongo abelii	19	50	2.63	12	1.00	1	2.63
207598	Homininae	147	369	2.51	9	2.26	3	1.11
9598	Pan troglodytes	2	4	2.00	2	1.00	1	2.00
9606	Homo sapiens	3	7	2.33	3	1.00	1	2.33
9593	Gorilla gorilla	15	43	2.87	7	1.00	1	2.87
9483	Callithrix jacchus	3	8	2.67	4	1.00	1	2.67
30608	Microcebus murinus	4	10	2.50	3	1.00	1	2.50
314145	Laurasiatheria	46	110	2.39	7	2.22	3	1.08
9397	Chiroptera	1	2	2.00	2	2.00	2	1.00
132908	Pteropus vampyrus	1	2	2.00	2	1.00	1	2.00
59463	Myotis lucifugus	2	8	4.00	6	1.00	1	4.00
9685	Felis catus	1	2	2.00	2	1.00	1	2.00
379584	Caniformia	41	85	2.07	4	2.00	2	1.04
9615	Canis familiaris	1	10	10.00	10	1.00	1	10.00
9796	Equus caballus	137	723	5.28	27	1.00	1	5.28
9362	Insectivora	2	16	8.00	14	2.00	2	4.00
42254	Sorex araneus	5	14	2.80	4	1.00	1	2.80
9365	Erinaceus europaeus	4	8	2.00	2	1.00	1	2.00
91561	Cetartiodactyla	11	32	2.91	8	2.00	2	1.45
30538	Vicugna pacos	3	10	3.33	6	1.00	1	3.33
9823	Sus scrofa	16	35	2.19	4	1.00	1	2.19
9913	Bos taurus	7	31	4.43	11	1.00	1	4.43
9739	Tursiops truncatus	1	2	2.00	2	1.00	1	2.00
311790	Afrotheria	4	8	2.00	2	2.00	2	1.00
9785	Loxodonta africana	5	23	4.60	14	1.00	1	4.60
9813	Procavia capensis	1	2	2.00	2	1.00	1	2.00
9371	Echinops telfairi	22	93	4.23	17	1.00	1	4.23
9263	Marsupialia	18	97	5.39	29	2.22	3	2.43
13616	Monodelphis domestica	16	74	4.63	10	1.00	1	4.63
9305	Sarcophilus harrisii	37	119	3.22	15	1.00	1	3.22
9315	Macropus eugenii	2	4	2.00	2	1.00	1	2.00
8364	Xenopus tropicalis	47	469	9.98	31	1.00	1	9.98
186625	Clupeocephala	332	2877	8.67	293	3.83	7	2.01
123370	Holacanthopterygii	440	1221	2.78	23	2.35	6	1.16
32485	Percomorpha	96	574	5.98	141	2.59	5	2.04
31031	Tetraodontidae	6	12	2.00	2	2.00	2	1.00
99883	Tetraodon nigroviridis	21	54	2.57	7	1.00	1	2.57
31033	Takifugu rubripes	2	4	2.00	2	1.00	1	2.00
129949	Smegmamorpha	35	82	2.34	8	2.00	2	1.17
69293	Gasterosteus aculeatus	26	111	4.27	15	1.00	1	4.27
8090	Oryzias latipes	84	373	4.44	23	1.00	1	4.44
8128	Oreochromis niloticus	21	110	5.24	22	1.00	1	5.24
8049	Gadus morhua	21	108	5.14	15	1.00	1	5.14
7955	Danio rerio	118	816	6.92	173	1.00	1	6.92
7718	Ciona	1352	3803	2.81	53	2.00	2	1.41
7719	Ciona intestinalis	164	457	2.79	15	1.00	1	2.79
51511	Ciona savignyi	81	220	2.72	6	1.00	1	2.72
7227	Drosophila melanogaster	485	1983	4.09	36	1.00	1	4.09
6239	Caenorhabditis elegans	1262	6862	5.44	37	1.00	1	5.44
4932	Saccharomyces cerevisiae	376	1143	3.04	20	1.00	1	3.04
	Total	19562	1000004	51.12	400	23.45	58	2.36

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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	nb_gene_splits	avg_dupscore	avg_dupscore_nondub
33154	Opisthokonta	2531	2347	184	0	0	0.90	0.90
33213	Bilateria	8605	5602	2664	339	0	0.57	0.57
33316	Coelomata	7620	6103	1280	237	0	0.48	0.48
7711	Chordata	9427	7510	1681	236	0	0.41	0.41
7742	Vertebrata	12216	7678	3803	735	0	0.49	0.49
7757	Petromyzon marinus	1814	0	1763	0	51	1.00	1.00
117571	Euteleostomi	25828	17468	6605	1755	0	0.43	0.43
8287	Sarcopterygii	17308	14851	875	1582	0	0.23	0.23
7897	Latimeria chalumnae	2779	0	2610	0	169	1.00	1.00
32523	Tetrapoda	14059	12923	614	522	0	0.27	0.27
32524	Amniota	19153	16550	1211	1392	0	0.22	0.22
32561	Sauria	11709	11557	130	22	0	0.47	0.47
28377	Anolis carolinensis	2139	0	1831	0	308	1.00	1.00
8825	Neognathae	13032	12833	185	14	0	0.61	0.61
9005	Phasianidae	12299	12098	201	0	0	0.71	0.71
9103	Meleagris gallopavo	430	0	192	0	238	1.00	1.00
9031	Gallus gallus	1025	0	919	0	106	1.00	1.00
59729	Taeniopygia guttata	2793	0	2537	0	256	1.00	1.00
40674	Mammalia	15424	13105	1164	1155	0	0.28	0.28
9258	Ornithorhynchus anatinus	2452	0	2135	0	317	1.00	1.00
32525	Theria	19734	17234	1409	1091	0	0.31	0.31
9347	Eutheria	110241	78935	5739	25567	0	0.18	0.18
9348	Xenarthra	6986	6933	53	0	0	0.69	0.69
9361	Dasypus novemcinctus	915	0	905	0	10	1.00	1.00
9358	Choloepus hoffmanni	597	0	594	0	3	1.00	1.00
314146	Euarchontoglires	43559	38373	605	4581	0	0.23	0.23
37347	Tupaia belangeri	870	0	847	0	23	1.00	1.00
314147	Glires	15232	14453	86	693	0	0.35	0.35
9989	Rodentia	13852	13235	79	538	0	0.47	0.47
33553	Sciurognathi	21200	21121	74	5	0	0.57	0.57
10020	Dipodomys ordii	492	0	478	0	14	1.00	1.00
39107	Murinae	18684	17395	1289	0	0	0.83	0.83
10090	Mus musculus	2781	0	2773	0	8	1.00	1.00
10116	Rattus norvegicus	2803	0	2685	0	118	1.00	1.00
43179	Ictidomys tridecemlineatus	1317	0	1023	0	294	1.00	1.00
10141	Cavia porcellus	1450	0	1383	0	67	1.00	1.00
9975	Lagomorpha	10538	10442	96	0	0	0.68	0.68
9978	Ochotona princeps	587	0	562	0	25	1.00	1.00
9986	Oryctolagus cuniculus	1857	0	1777	0	80	1.00	1.00
9443	Primates	17716	17187	163	366	0	0.32	0.32
376913	Haplorrhini	9079	9000	49	30	0	0.41	0.41
9478	Tarsius syrichta	509	0	503	0	6	1.00	1.00
314293	Simiiformes	18728	17658	897	173	0	0.44	0.44
9526	Catarrhini	18902	17770	847	285	0	0.41	0.41
9544	Macaca mulatta	1613	0	1351	0	262	1.00	1.00
314295	Hominoidea	17458	16883	259	316	0	0.40	0.40
9604	Hominidae	17646	17289	265	92	0	0.49	0.49
9601	Pongo abelii	460	0	416	0	44	1.00	1.00
207598	Homininae	34278	33949	329	0	0	0.61	0.61
9598	Pan troglodytes	233	0	220	0	13	1.00	1.00
9606	Homo sapiens	570	0	564	0	6	1.00	1.00
9593	Gorilla gorilla	612	0	569	0	43	1.00	1.00
61853	Nomascus leucogenys	191	0	135	0	56	1.00	1.00
9483	Callithrix jacchus	1586	0	1497	0	89	1.00	1.00
376911	Strepsirrhini	10169	10143	26	0	0	0.73	0.73
30611	Otolemur garnettii	1283	0	1235	0	48	1.00	1.00
30608	Microcebus murinus	472	0	442	0	30	1.00	1.00
314145	Laurasiatheria	72344	69241	508	2595	0	0.24	0.24
9397	Chiroptera	9481	9474	7	0	0	0.50	0.50
132908	Pteropus vampyrus	294	0	267	0	27	1.00	1.00
59463	Myotis lucifugus	2738	0	2656	0	82	1.00	1.00
33554	Carnivora	11609	11505	51	53	0	0.47	0.47
9685	Felis catus	220	0	200	0	20	1.00	1.00
379584	Caniformia	14833	14653	180	0	0	0.68	0.68
9646	Ailuropoda melanoleuca	569	0	485	0	84	1.00	1.00
9615	Canis familiaris	1204	0	943	0	261	1.00	1.00
9796	Equus caballus	2231	0	2121	0	110	1.00	1.00
9362	Insectivora	5048	5021	27	0	0	0.70	0.70
42254	Sorex araneus	911	0	900	0	11	1.00	1.00
9365	Erinaceus europaeus	601	0	593	0	8	1.00	1.00
91561	Cetartiodactyla	36360	36155	205	0	0	0.53	0.53
30538	Vicugna pacos	251	0	237	0	14	1.00	1.00
9823	Sus scrofa	3170	0	2604	0	566	1.00	1.00
9913	Bos taurus	1644	0	1592	0	52	1.00	1.00
9739	Tursiops truncatus	185	0	163	0	22	1.00	1.00
311790	Afrotheria	20924	20773	151	0	0	0.65	0.65
9785	Loxodonta africana	2164	0	2006	0	158	1.00	1.00
9813	Procavia capensis	349	0	336	0	13	1.00	1.00
9371	Echinops telfairi	1197	0	1179	0	18	1.00	1.00
9263	Marsupialia	28975	28070	905	0	0	0.66	0.66
13616	Monodelphis domestica	2095	0	1946	0	149	1.00	1.00
9305	Sarcophilus harrisii	1330	0	1193	0	137	1.00	1.00
9315	Macropus eugenii	525	0	517	0	8	1.00	1.00
8364	Xenopus tropicalis	3284	0	3236	0	48	1.00	1.00
186625	Clupeocephala	22327	17957	4189	181	0	0.63	0.63
123370	Holacanthopterygii	19037	17674	839	524	0	0.55	0.55
32485	Percomorpha	41371	35915	572	4884	0	0.45	0.45
31031	Tetraodontidae	15742	15551	191	0	0	0.69	0.69
99883	Tetraodon nigroviridis	1472	0	1294	0	178	1.00	1.00
31033	Takifugu rubripes	1019	0	979	0	40	1.00	1.00
129949	Smegmamorpha	9915	9901	14	0	0	0.57	0.57
69293	Gasterosteus aculeatus	1381	0	1263	0	118	1.00	1.00
8090	Oryzias latipes	1366	0	1217	0	149	1.00	1.00
8128	Oreochromis niloticus	2192	0	2187	0	5	1.00	1.00
8049	Gadus morhua	1210	0	1087	0	123	1.00	1.00
7955	Danio rerio	5529	0	5401	0	128	1.00	1.00
7718	Ciona	9596	8107	1489	0	0	0.78	0.78
7719	Ciona intestinalis	1719	0	1437	0	282	1.00	1.00
51511	Ciona savignyi	1154	0	936	0	218	1.00	1.00
7227	Drosophila melanogaster	3855	0	3855	0	0	1.00	1.00
6239	Caenorhabditis elegans	8512	0	8492	0	20	1.00	1.00
4932	Saccharomyces cerevisiae	1281	0	1266	0	15	1.00	1.00
	Total (ancestral species)	890775	798622	42190	49963	0	0.45	0.45
	Total (extant species)	90282	0	84534	0	5748	1.00	1.00
	Total	981057	798622	126724	49963	5748	0.82	0.82