First commit after compilation

README.md

@@ -1,2 +1,11 @@
-# rbps_evo
 Analysis of  SRRM2, SON, PRPF8, SRRM1, RBM25, Pinin and Coilin orthologues
+
+# contents:
+data
+results
+fig
+
+Notebooks:
+- dataset preparation and length comparison
+- disorder prediction
+

data/TimeTree.nwk

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+((((((((((((((((((((((Pan_troglodytes:2.8200595,Pan_paniscus:2.8200595)475:3.8308456,Homo_sapiens:6.650905)455:2.4121904,Gorilla_gorilla:9.063095)481:6.69907,Pongo_abelii:15.762165)480:13.679381,((Mandrillus_leucophaeus:4.5903716,Cercocebus_atys:4.5903716)373:14.831933,Piliocolobus_tephrosceles:19.422304):10.019242)487:13.709749,Aotus_nancymaae:43.151295)485:30.685598,Microcebus_murinus:73.83689)452:15.986293,(((Rattus_norvegicus:20.887417,Mus_musculus:20.887417)408:51.989292,Chinchilla_lanigera:72.87671)434:9.264091,Oryctolagus_cuniculus:82.1408)428:7.6823883)495:6.6392016,(((((((Ursus_arctos:39.893414,Phoca_vitulina:39.893414)298:5.634937,Canis_lupus:45.52835)296:8.793092,Felis_catus:54.32144)301:22.905153,Ceratotherium_simum:77.22659)294:0.5283624,((((Ovis_aries:24.6,Bos_taurus:24.6)342:31.359854,Orcinus_orca:55.959854)350:6.0061355,Sus_scrofa:61.96599)353:2.2180355,(Vicugna_pacos:20.56159,Camelus_dromedarius:20.56159)316:43.622433)349:13.570932)339:0.77378565,(((Rousettus_aegyptiacus:27.380796,Pteropus_vampyrus:27.380796)361:30.697678,Hipposideros_armiger:58.078476)357:3.5827332,((Eptesicus_fuscus:31.322325,Myotis_brandtii:31.322325)364:21.323698,Phyllostomus_discolor:52.646023)338:9.015184)292:16.867535)377:10.795076,Erinaceus_europaeus:89.32382)375:7.138571)493:8.997392,((Elephantulus_edwardii:74.53317,Chrysochloris_asiatica:74.53317)503:8.755768,Loxodonta_africana:83.28894)507:22.170837)510:53.137806,Sarcophilus_harrisii:158.59758)506:18.32991,Ornithorhynchus_anatinus:176.9275)500:134.97643,(((((((((Pseudopodoces_humilis:26.075,Parus_major:26.075)158:16.703297,(Catharus_ustulatus:34.2,Ficedula_albicollis:34.2)124:8.578296)157:0.92170393,(Taeniopygia_guttata:38.0,Camarhynchus_parvulus:38.0)119:5.7)118:39.409245,(Aquila_chrysaetos:82.1,Columba_livia:82.1):1.0092447)229:14.933624,(Anas_platyrhynchos:79.955414,Gallus_gallus:79.955414)136:18.087454)225:13.310755,(Apteryx_rowi:62.336754,Dromaius_novaehollandiae:62.336754)100:49.01687)224:125.14904,(Crocodylus_porosus:80.36866,Alligator_sinensis:80.36866)242:156.134)241:17.231544,(Chelonia_mydas:100.65272,Chrysemys_picta:100.65272)239:153.08148)250:25.922768,(((((Pseudonaja_textilis:51.393105,Thamnophis_elegans:51.393105)92:10.3449745,Protobothrops_mucrosquamatus:61.73808)71:105.38611,(Anolis_carolinensis:157.41875,Pogona_vitticeps:157.41875)69:9.705438)65:10.872629,Podarcis_muralis:177.99683)25:23.00318,Gekko_japonicus:201.0)102:78.656975)238:32.246944)499:39.85456,(Xenopus_laevis:56.62137,Xenopus_tropicalis:56.62137)73:295.13712)449:61.230156,Latimeria_chalumnae:412.98865)520:22.335434,(((((((((Poecilia_reticulata:42.2,Poecilia_mexicana:42.2)14:0.0,Xiphophorus_couchianus:42.2)13:50.972317,Oryzias_latipes:93.17232)11:26.191216,(((Amphiprion_ocellaris:67.061844,Stegastes_partitus:67.061844)10:30.33816,(Gouania_willdenowi:77.0,Salarias_fasciatus:77.0)19:20.4)9:13.607928,(Maylandia_zebra:2.68059,Pundamilia_nyererei:2.68059)22:108.32734)8:8.355604)6:8.636468,((((Cottoperca_gobio:76.0,Notothenia_coriiceps:76.0)27:0.0,Anarrhichthys_ocellatus:76.0)35:34.0,Takifugu_rubripes:110.0)42:0.0,((Seriola_lalandi:29.2,Seriola_dumerili:29.2)30:54.346184,Scophthalmus_maximus:83.54618)29:26.453817)40:18.0)48:4.0,Myripristis_murdjan:132.0)51:16.0,Gadus_morhua:148.0)47:58.335457,((((Oncorhynchus_mykiss:14.247032,Oncorhynchus_kisutch:14.247032)39:8.171497,Salvelinus_alpinus:22.41853)56:23.30358,Salmo_salar:45.72211)55:81.8209,Esox_lucius:127.543015)61:78.79245)60:23.567303,((((((Pangasianodon_hypophthalmus:64.83749,Ictalurus_punctatus:64.83749)54:85.16251,Pygocentrus_nattereri:150.0)38:0.0,Electrophorus_electricus:150.0)34:2.5854318,Danio_rerio:152.58543)26:33.41457,Chanos_chanos:186.0)66:35.73315,Denticeps_clupeoides:221.73315)75:8.169611)80:205.42131)518:37.981285,Callorhinchus_milii:473.30536)523:203.14253,Ciona_intestinalis:676.4479)517:7.5521,Branchiostoma_floridae:684.0)528:112.55565,(((((((((((((((((((Trachymyrmex_cornetzi:11.0,Trachymyrmex_septentrionalis:11.0)550:5.0,Trachymyrmex_zeteki:16.0)548:12.06861,Atta_cephalotes:28.06861)526:16.428198,Cyphomyrmex_costatus:44.496807)516:40.40319,Vollenhovia_emeryi:84.9)448:0.0,Wasmannia_auropunctata:84.9)555:4.3,Pogonomyrmex_barbatus:89.2)553:1.8,(Solenopsis_invicta:91.0,Monomorium_pharaonis:91.0)447:0.0)445:19.704554,Camponotus_floridanus:110.70455)566:21.295446,Pseudomyrmex_gracilis:132.0)564:30.0,((((((Apis_mellifera:18.475,Apis_cerana:18.475)539:0.06406,Apis_dorsata:18.53906)538:83.46094,Eufriesea_mexicana:102.0)534:0.0,Ceratina_calcarata:102.0)533:8.0,Habropoda_laboriosa:110.0)531:0.0,Dufourea_novaeangliae:110.0)527:52.0)570:73.0,Orussus_abietinus:235.0)573:90.056984,(((((((Papilio_machaon:23.571804,Papilio_xuthus:23.571804)598:2.6456118,Papilio_polytes:26.217415)597:79.782585,Bicyclus_anynana:106.0)596:8.156975,(Bombyx_mori:67.38167,Manduca_sexta:67.38167)599:46.775307)594:63.843025,Hyposmocoma_kahamanoa:178.0)582:94.0,((((Musca_domestica:34.6,Stomoxys_calcitrans:34.6)562:20.102293,Lucilia_cuprina:54.702293)587:77.29771,((Drosophila_melanogaster:33.863625,Drosophila_ananassae:33.863625)586:92.136375,Bactrocera_dorsalis:126.0)591:6.0)585:140.0,((Aedes_albopictus:37.06975,Aedes_aegypti:37.06975)563:112.93025,Culex_quinquefasciatus:150.0)576:122.0)583:0.0)610:38.188473,Tribolium_castaneum:310.18848)608:14.868513)613:32.531662,(Pediculus_humanus:344.0,Acyrthosiphon_pisum:344.0)607:13.588651)620:0.17157616,(Cryptotermes_secundus:132.08488,Zootermopsis_nevadensis:132.08488)619:225.67535)618:172.23978,((Eurytemora_affinis:530.0,Daphnia_magna:530.0)541:0.0,Litopenaeus_vannamei:530.0)540:0.0)617:71.00586,((Dermatophagoides_pteronyssinus:494.0,Metaseiulus_occidentalis:494.0)626:0.0,Parasteatoda_tepidariorum:494.0)616:107.00586)606:141.99414,((((Caenorhabditis_brenneri:18.6,Caenorhabditis_elegans:18.6)630:41.6,(Caenorhabditis_briggsae:17.2,Caenorhabditis_remanei:17.2)635:43.0)639:180.5403,Brugia_malayi:240.7403)638:187.539,Trichinella_pseudospiralis:428.2793)634:314.7207)643:10.0,(((((Crassostrea_virginica:72.91005,Crassostrea_gigas:72.91005)629:382.08994,Mizuhopecten_yessoensis:455.0)605:82.31917,Aplysia_californica:537.31915)581:56.46071,(Octopus_bimaculoides:3.68,Octopus_vulgaris:3.68)646:590.09985)580:93.93952,(Helobdella_robusta:602.0,Capitella_teleta:602.0)633:85.7194)651:65.2806)649:43.55565)579:27.444353,((((((Stylophora_pistillata:43.309513,Pocillopora_damicornis:43.309513)561:206.82913,Acropora_millepora:250.13866)559:83.86135,Montastraea_faveolata:334.0)671:235.34184,Nematostella_vectensis:569.34186)675:47.65816,Dendronephthya_gigantea:617.0)674:0.0,Hydra_vulgaris:617.0)670:207.0)669:127.825,Amphimedon_queenslandica:951.825);

data/TimeTree_pruned.nwk

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+((((((((((((((((((Pan_troglodytes:6.6509051,Homo_sapiens:6.650905)455:2.4121904,Gorilla_gorilla:9.063095)481:6.69907,Pongo_abelii:15.762165)480:13.679381,(Cercocebus_atys:19.4223046,Piliocolobus_tephrosceles:19.422304):10.019242)487:44.395347,Microcebus_murinus:73.83689)452:15.986293,(((Rattus_norvegicus:20.887417,Mus_musculus:20.887417)408:51.989292,Chinchilla_lanigera:72.87671)434:9.264091,Oryctolagus_cuniculus:82.1408)428:7.6823883)495:6.6392016,((((((Ursus_arctos:39.893414,Phoca_vitulina:39.893414)298:5.634937,Canis_lupus:45.52835)296:8.793092,Felis_catus:54.32144)301:22.905153,Ceratotherium_simum:77.22659)294:0.5283624,((((Ovis_aries:24.6,Bos_taurus:24.6)342:31.359854,Orcinus_orca:55.959854)350:6.0061355,Sus_scrofa:61.96599)353:2.2180355,(Vicugna_pacos:20.56159,Camelus_dromedarius:20.56159)316:43.622433)349:13.570932)339:0.77378565,((Pteropus_vampyrus:58.078474,Hipposideros_armiger:58.078476)357:3.5827332,((Eptesicus_fuscus:31.322325,Myotis_brandtii:31.322325)364:21.323698,Phyllostomus_discolor:52.646023)338:9.015184)292:16.867535)377:17.933647)493:8.997392,Elephantulus_edwardii:105.459775)510:53.137806,Sarcophilus_harrisii:158.59758)506:18.32991,Ornithorhynchus_anatinus:176.9275)500:134.97643,((((((((Pseudopodoces_humilis:26.075,Parus_major:26.075)158:16.703297,Ficedula_albicollis:42.778296)157:0.92170393,(Taeniopygia_guttata:38,Camarhynchus_parvulus:38)119:5.7)118:39.409245,(Aquila_chrysaetos:82.1,Columba_livia:82.1):1.0092447)229:14.933624,(Anas_platyrhynchos:79.955414,Gallus_gallus:79.955414)136:18.087454)225:13.310755,Dromaius_novaehollandiae:111.353624)224:142.380584,Chrysemys_picta:253.7342)250:25.922768,(((((Pseudonaja_textilis:51.393105,Thamnophis_elegans:51.393105)92:10.3449745,Protobothrops_mucrosquamatus:61.73808)71:105.38611,Pogona_vitticeps:167.124188)65:10.872629,Podarcis_muralis:177.99683)25:23.00318,Gekko_japonicus:201)102:78.656975)238:32.246944)499:39.85456,(Xenopus_laevis:56.62137,Xenopus_tropicalis:56.62137)73:295.13712)449:61.230156,Latimeria_chalumnae:412.98865)520:22.335434,((((Poecilia_reticulata:42.2,Poecilia_mexicana:42.2)14:77.163533,Maylandia_zebra:119.363534)6:86.971925,((Oncorhynchus_mykiss:45.722109,Salmo_salar:45.72211)55:81.8209,Esox_lucius:127.543015)61:78.79245)60:23.567303,((Ictalurus_punctatus:150,Pygocentrus_nattereri:150)38:2.5854318,Danio_rerio:152.58543)26:77.317331)80:205.42131)518:248.675915,Branchiostoma_floridae:684)528:112.55565,(((((((((Trachymyrmex_septentrionalis:28.06861,Atta_cephalotes:28.06861)526:16.428198,Cyphomyrmex_costatus:44.496807)516:66.207744,Camponotus_floridanus:110.70455)566:51.295446,(((Apis_mellifera:102,Eufriesea_mexicana:102)534:8,Habropoda_laboriosa:110)531:0,Dufourea_novaeangliae:110)527:52)570:163.056984,(((Musca_domestica:132.000003,(Drosophila_melanogaster:33.863625,Drosophila_ananassae:33.863625)586:98.136375)585:140,Aedes_albopictus:272)583:38.188473,Tribolium_castaneum:310.18848)608:14.868513)613:32.531662,(Pediculus_humanus:344,Acyrthosiphon_pisum:344)607:13.588651)620:0.17157616,Cryptotermes_secundus:357.76023)618:385.23978,(Caenorhabditis_elegans:240.7403,Brugia_malayi:240.7403)638:502.2597)643:10,(Crassostrea_gigas:537.31916,Aplysia_californica:537.31915)581:215.68083)649:43.55565)579:27.444353,(Pocillopora_damicornis:569.341833,Nematostella_vectensis:569.34186)675:254.65816)669:127.825,Amphimedon_queenslandica:951.825);