diff --git a/README.markdown b/README.markdown index 44c9c45..08109ef 100644 --- a/README.markdown +++ b/README.markdown @@ -85,4 +85,44 @@ Note that download_and_filter_wikidata and download_and_filter_pageviews take se 4. Commit `dvc.lock` to git. + +## Uploading tree to server + +1. If you are running the tree building scripts on a different computer to the one running the web server, you will need to push the `completetree_XXXXXX.js`, `completetree_XXXXXX.js.gz`, `cut_position_map_XXXXXX.js`, `cut_position_map_XXXXXX.js.gz`, `dates_XXXXXX.js`, `dates_XXXXXX.js.gz` files onto your server, e.g. by pushing to your local Github repo then pulling the latest github changes to the server. + +2. (15 mins) load the CSV tables into the DB. Use the script generated in `data/output_files/import_XXXXXX.sql` to truncate and repopulate ordered_leaves/nodes/etc. + + ``` + echo "SET GLOBAL local_infile=ON;" | mysql -p OneZoom_dev + mysql --local-infile --host localhost --user onezoom --password --database OneZoom_dev < data/output_files/import_XXXXXX.sql + ``` + +3. Check for dups, and if any sponsors are no longer on the tree, using something like the following SQL command: + + ``` + select * from reservations left outer join ordered_leaves on reservations.OTT_ID = ordered_leaves.ott where ordered_leaves.ott is null and reservations.verified_name IS NOT NULL; + select group_concat(id), group_concat(parent), group_concat(name), count(ott) from ordered_leaves group by ott having(count(ott) > 1) + ``` + +### Fill in additional server fields + + 11. (15 mins) create example pictures for each node by percolating up. This requires the most recent `images_by_ott` table, so either do this on the main server, or (if you are doing it locally) update your `images_by_ott` to the most recent server version. + + ``` + ${OZ_DIR}/OZprivate/ServerScripts/Utilities/picProcess.py -v + ``` + +1. (5 mins) percolate the IUCN data up using + + ``` + ${OZ_DIR}/OZprivate/ServerScripts/Utilities/IUCNquery.py -v + ``` + + (note that this both updates the IUCN data in the DB and percolates up interior node info) + +1. (10 mins) If this is a site with sponsorship (only the main OZ site), set the pricing structure using SET_PRICES.html (accessible from the management pages). +1. (5 mins - this does seem to be necessary for ordered nodes & ordered leaves). Make sure indexes are reset. Look at `OZprivate/ServerScripts/SQL/create_db_indexes.sql` for the SQL to do this - this may involve logging in to the SQL server (e.g. via Sequel Pro on Mac) and pasting all the drop index and create index commands. + + + For detailed step-by-step documentation, see [oz_tree_build/README.markdown](oz_tree_build/README.markdown). diff --git a/data/OZTreeBuild/AllLife/BespokeTree/include_noAutoOTT/Deepfin2.phy b/data/OZTreeBuild/AllLife/BespokeTree/include_noAutoOTT/Deepfin2.phy index 5f583aa..b07641d 100755 --- a/data/OZTreeBuild/AllLife/BespokeTree/include_noAutoOTT/Deepfin2.phy +++ b/data/OZTreeBuild/AllLife/BespokeTree/include_noAutoOTT/Deepfin2.phy @@ -1,4 +1,4 @@ [DeepFin2/3 phylogeny https://doi.org/10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288 , with a few branches extracted to other files (those ending with @) #from https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#contexts to help add OTTids: context=Vertebrates] -(((COELACANTHIFORMES@,(DIPNOI@,TETRAPODA@)Dipnotetrapodomorpha:27.5)Sarcopterygii:15.4,(POLYPTERIFORMES@,(ACIPENSERIFORMES@,(HOLOSTEI@,(((Megalops_atlanticus:133.591899,Elops_saurus:133.591899)Elopiformes:62.608101,((Albula_glossodonta:40.548584,Albula_vulpes:40.548584)Albuliformes:110.251416,((Notacanthus_chemnitzii:50.676944,(Halosauropsis_macrochir:40.373487,Aldrovandia_affinis:40.373487):10.303457)Notacanthiformes:50.323056,(((Eurypharynx_pelecanoides:25.868725,Saccopharynx_ampullaceus:25.868725):44.324932,(Nemichthys_scolopaceus:58.74446,Anguilla_rostrata:58.74446):11.449197):9.198477,((Serrivomer_beanii:53.005541,Echidna_nebulosa_rhodochilus:53.005541):23.052738,(Conger_oceanicus:65.421519,(Muraenesox_cinereus:57.198765,(Myrichthys_maculosus:35.64527,Ophichthus_cephalozona:35.64527):21.553495):8.222754):10.63676):3.333855)Anguilliformes:21.607866):49.8):45.4)Elopomorpha:87.1,(((Hiodon_tergisus:9.532829,Hiodon_alosoides:9.532829)Hiodontiformes:217.567171,(Pantodon_buchholzi:163.1,((Osteoglossum_bicirrhosum:104.854707,(Arapaima_gigas:78.299999,Heterotis_niloticus:78.299999):26.554708):43.473236,((Gnathonemus_petersii:78.30036,Gymnarchus_niloticus:78.30036):41.99964,(Xenomystus_nigri:81.631435,(Chitala_chitala:1.219286,Chitala_ornata:1.219286):80.412149):38.668565):28.027943):14.772057)Osteoglossiformes:64.0)Osteoglossomorpha:46.7,(((Denticeps_clupeoides:188.9,(Jenkinsia_lamprotaenia:105.3,(Chirocentrus_dorab:87.117111,((Engraulis_mordax_eurystole:47.084649,Coilia_nasus:47.084649):33.352669,((Pellona_flavipinnis:27.465346,Ilisha_elongata:27.465346):46.442845,(Alosa_pseudoharengus:54.162778,Dorosoma_cepedianum:54.162778):19.745413):6.529127):6.679793):18.182889):83.6)Clupeiformes:41.3,((Talismania_bifurcata:53.278988,((Bathylaco_nigricans:33.838039,(Alepocephalus_tenebrosus:4.64507,Alepocephalus_agassizii:4.64507):29.192969):10.957021,((Rouleina_attrita:22.280783,Xenodermichthys_copei:22.280783):19.919217,(Sagamichthys_abei:16.923695,(Searsia_koefoedi:16.870939,(Maulisia_microlepis:12.550045,Normichthys_operosus:12.550045):4.320894):0.052756):25.276305):2.59506):8.483928)Alepocephaliformes:166.419559,(((Gonorynchus_abbreviatus:18.169743,(Gonorynchus_greyi:2.712754,Gonorynchus_forsteri:2.712754):15.456989):157.730257,(Chanos_chanos:147.1,(Phractolaemus_ansorgii:99.074809,(Parakneria_sp:30.990181,Cromeria_nilotica:30.990181):68.084628):48.025191):28.8)Gonorynchiformes:22.7,((((Gyrinocheilus_sp:70.113283,(Hypentelium_nigricans:23.597192,(Carpiodes_carpio:16.357477,Ictiobus_bubalus:16.357477):7.239715):46.516091):8.686717,(Botia_sp:62.783932,((Cobitis_taenia:30.34787,Cobitis_lutheri:30.34787):24.685854,(Barbatula_barbatula:35.045041,Traccatichthys_pulcher:35.045041):19.988683):7.750208):16.016068):20.5,(Danio_rerio:63.3,(((Opsariichthys_uncirostris_bidens:12.731429,Zacco_sieboldii_platypus:12.731429):14.613577,((Xenocypris_argentea:12.908174,Hypophthalmichthys_molitrix:12.908174):2.918337,(Luciobrama_macrocephalus:13.443807,(Squaliobarbus_curriculus:11.476351,Mylopharyngodon_piceus:11.476351):1.967456):2.382704):11.518495):12.402485,(Tanakia_lanceolata_himantegus:35.011399,(Notemigonus_crysoleucas:22.938856,(Semotilus_atromaculatus:21.330371,((Campostoma_oligolepis:12.804185,Rhinichthys_cataractae:12.804185):4.409637,(Phenacobius_uranops:12.825815,(Pimephales_promelas_notatus:9.462704,(Luxilus_coccogenis:6.740554,Notropis_asperifrons:6.740554):2.72215):3.363111):4.388007):4.116549):1.608485):12.072543):4.736092):23.552509):36.0)Cypriniformes:73.6,((Apteronotus_albifrons:69.0,(Electrophorus_electricus:63.911009,(Sternopygus_macrurus:60.837773,((Gymnorhamphichthys_petiti:36.693003,Rhamphichthys_sp:36.693003):20.733429,(Gymnotus_sp:54.517707,Eigenmannia_macrops:54.517707):2.908725):3.411341):3.073236):5.088991)Gymnotiformes:78.834643,(((Distichodus_maculatus:103.608884,(Citharinus_congicus:79.291248,(Boulengerella_maculata:58.556224,Chilodus_punctatus:58.556224):20.735024):24.317636):11.169648,((Characidium_pterostictum:94.400719,(Phenacogrammus_interruptus:41.476061,Alestes_baremoze:41.476061):52.924658):12.270302,(Hepsetus_odoe:100.958204,((Hoplias_sp:85.128079,((Hydrolycus_scomberoides:67.534284,(Parodon_nasus:57.90201,Pygocentrus_nattereri:57.90201):9.632274):1.265716,(Hemiodus_immaculatus:61.520855,(Prochilodus_magdalenae_lineatus:24.799731,Semaprochilodus_insignis:24.799731):36.721124):7.279145):16.328079):6.090114,(Pyrrhulina_australis:87.546225,(Chalceus_macrolepidotus:75.175356,((Brycon_pesu_sp:66.005816,(Triportheus_nematurus:61.149028,(Thoracocharax_stellatus:27.747849,Gasteropelecus_sternicla:27.747849):33.401179):4.856788):1.227233,(Acestrorhynchus_falcatus:63.186555,(Spintherobolus_ankoseion:50.022124,((Bryconamericus_emperador:22.448614,Markiana_nigripinnis:22.448614):21.013331,(Nematobrycon_palmeri:30.437296,Astyanax_mexicanus:30.437296):13.024649):6.560179):13.164431):4.046494):7.942307):12.370869):3.671968):9.740011):5.712817):8.107511)Characiformes:22.233622,((Nematogenys_inermis:110.648979,(Trichomycterus_sp:105.886773,((Loricaria_simillima:70.314063,Astroblepus_sp:70.314063):28.122065,(Callichthys_callichthys:69.2,(Corydoras_trilineatus:40.456696,Corydoras_aurofrenatus:40.456696):28.743304):29.236128):7.450645):4.762206):5.151021,(Diplomystes_nahuelbutaensis:106.204156,((Clarias_batrachus:47.601763,Heteropneustes_fossilis:47.601763):38.718355,(((Bagarius_yarrelli:55.522683,(Liobagrus_aequilabris:48.028166,Akysis_sp:48.028166):7.494517):21.359019,((Horabagrus_brachysoma:59.629878,Pseudeutropius_brachypopterus:59.629878):14.819689,(Mystus_bocourti:36.078433,Bagrus_ubangensis:36.078433):38.371134):2.432135):8.407973,(((Chaca_sp:72.429965,(Helogenes_marmoratus:57.16588,Cetopsis_coecutiens:57.16588):15.264085):10.714848,(Cranoglanis_bouderius:68.699999,(Ictalurus_punctatus:39.099999,Ameiurus_natalis:39.099999):29.6):14.444814):1.039632,((Pangasianodon_hypophthalmus:80.594984,(Gogo_arcuatus:69.1,Ariopsis_felis_seemanni:69.1):11.494984):1.563582,(((Chrysichthys_sp:6.269994,Chrysichthys_dendrophorus:6.269994):67.584437,(Amphilius_jacksonii:69.200236,(Malapterurus_beninensis:64.740777,Synodontis_batesii:64.740777):4.459459):4.654195):6.339371,((Plotosus_lineatus:73.040117,Hemisilurus_moolenburghi:73.040117):5.503896,((Ageneiosus_atronasus:51.102018,Anduzedoras_oxyrhynchus:51.102018):23.797937,(Goeldiella_eques:57.155894,(Pseudopimelodus_mangurus:46.825924,Brachyplatystoma_filamentosum:46.825924):10.32997):17.744061):3.644058):1.649789):1.964764):2.025879):1.10523):1.030443):19.884038):9.595844)Siluriformes:21.212154)Characiphysae:10.822489):25.065357)Otophysi:25.7)Ostariophysi:21.098547):10.501453)Otomorpha:20.4,(Lepidogalaxias_salamandroides:231.8,(((Bathylagus_euryops:70.712354,(Nansenia_longicauda_ardesiaca:51.558629,(Macropinna_microstoma:33.234078,(Argentina_sialis_silus:13.624567,Argentina_striata:13.624567):19.609511):18.324551):19.153725)Argentiniformes:88.887646,((Aplochiton_taeniatus:50.0,(Galaxiella_nigrostriata:42.605636,(Neochanna_burrowsius:34.522004,(Brachygalaxias_bullocki:32.495985,Galaxias_maculatus:32.495985):2.026019):8.083632):7.394364)Galaxiiformes:95.636629,(((Esox_lucius:31.386513,Esox_americanus:31.386513):48.013487,(Umbra_limi:55.772876,Novumbra_hubbsi:55.772876):23.627124)Esociformes:25.078403,(Coregonus_clupeaformis:35.3,(Thymallus_brevirostris:32.464307,(Oncorhynchus_nerka_mykiss:19.947525,(Salvelinus_alpinus:16.756184,(Salmo_salar:14.861468,Parahucho_perryi:14.861468):1.894716):3.191341):12.516782):2.835693)Salmoniformes:69.178403):41.158226):13.963371)Protacanthopterygii:55.254892,((((Retropinna_semoni:22.529514,Stokellia_anisodon:22.529514):51.170486,(((Osmerus_mordax:10.347393,Thaleichthys_pacificus:10.347393):5.877349,(Mallotus_villosus:14.980242,Hypomesus_pretiosus:14.980242):1.2445):18.137763,(Plecoglossus_altivelis:28.725469,((Neosalanx_jordani:10.487235,Neosalangichthys_ishikawae:10.487235):2.238638,(Salanx_cuvieri:7.987388,Leucosoma_reevesii:7.987388):4.738485):15.999596):5.637036):39.337495)Osmeriformes:55.7,((Diplophos_taenia:77.34295,((Bonapartia_pedaliota:54.320038,Margrethia_obtusirostra:54.320038):20.007411,(Gonostoma_elongatum:69.964426,Cyclothone_microdon:69.964426):4.363023):3.015501):6.45705,(Pollichthys_mauli:77.73342,((Polymetme_corythaeola_sp:67.565698,(Polyipnus_spinifer:60.02376,((Argyropelecus_gigas:10.75016,Argyropelecus_affinis:10.75016):14.493519,(Sternoptyx_sp:20.932156,Maurolicus_weitzmani:20.932156):4.311523):34.780081):7.541938):5.012869,((Chauliodus_sloani:20.419989,Chauliodus_macouni_danae:20.419989):42.727184,((Borostomias_antarcticus:23.038554,Neonesthes_capensis:23.038554):17.725111,((Heterophotus_ophistoma:34.302727,(Stomias_boa:27.141257,Rhadinesthes_decimus:27.141257):7.16147):1.805224,(Astronesthes_leucopogon:35.402261,(Chirostomias_pliopterus:31.596407,((Melanostomias_margaritifer:21.804032,Leptostomias_longibarba:21.804032):5.231986,((Photonectes_margarita:19.065425,Tactostoma_macropus:19.065425):7.217791,(Photostomias_guernei:24.056719,(Malacosteus_niger:23.385989,(Eustomias_polyaster:23.058022,(Aristostomias_scintillans:23.044458,Bathophilus_flemingi_pawneei:23.044458):0.013564):0.327967):0.67073):2.226497):0.752802):4.560389):3.805854):0.70569):4.655714):22.383508):9.431394):5.154853):6.06658)Stomiatiformes:45.6)Stomiatii:81.9,((Ateleopus_japonicus:8.100975,(Ijimaia_antillarum:1.851199,Ijimaia_loppei:1.851199):6.249776)Ateleopodiformes:184.199025,(((Synodus_variegatus:50.706529,(Trachinocephalus_myops:34.936529,Synodus_foetens:34.936529):15.77):63.193471,(((Pseudotrichonotus_altivelis:85.069082,Paraulopus_oblongus:85.069082):16.922086,(Saurida_gracilis:50.265907,(Harpadon_microchir:42.546554,Saurida_undosquamis:42.546554):7.719353):51.725261):8.324299,(((Aulopus_filamentosus:47.181996,Bathysaurus_ferox:47.181996):10.847641,(Bathypterois_grallator:52.456704,Ipnops_sp:52.456704):5.572933):23.632996,((Bathypterois_atricolor:69.35022,(Gigantura_indica:13.530161,Gigantura_chuni:13.530161):55.820059):6.463444,((Benthalbella_macropinna:31.410754,(Benthalbella_dentata:8.014963,Benthalbella_infans:8.014963):23.395791):31.100655,((Chlorophthalmus_agassizi:56.023798,Scopelarchus_sp:56.023798):5.132849,(Parasudis_truculenta:59.829934,((Ahliesaurus_berryi:25.638925,Scopelosaurus_lepidus:25.638925):33.459363,(Sudis_atrox:55.043996,((Anotopterus_pharao:45.676404,(Omosudis_lowii:36.295606,(Alepisaurus_brevirostris:28.879812,Alepisaurus_ferox:28.879812):7.415794):9.380798):8.24094,((Stemonosudis_intermedia_macrura:38.680633,Lestidiops_jayakari:38.680633):11.457751,((Evermannella_balbo:17.517053,Coccorella_atlantica:17.517053):29.184168,(Paralepis_coregonoides:36.168036,(Notolepis_coatsi:0.46445,Magnisudis_prionosa:0.46445):35.703586):10.533185):3.437163):3.77896):1.126652):4.054292):0.731646):1.326713):1.354762):13.302255):5.848969):28.652834):3.584533)Aulopiformes:68.9,((((Neoscopelus_macrolepidotus:21.513581,Neoscopelus_microchir:21.513581):20.906388,(Scopelengys_sp:5.004968,Scopelengys_tristis:5.004968):37.415001):31.180031,(((Notolychnus_valdiviae:40.191883,Lobianchia_gemellarii:40.191883):5.72165,(Lampadena_speculigera:39.826216,((Lepidophanes_guentheri:21.437275,(Ceratoscopelus_maderensis:10.546561,Ceratoscopelus_warmingii:10.546561):10.890714):16.309947,(Stenobrachius_leucopsarus:31.265086,(Nannobrachium_lineatum:26.763615,(Lampanyctus_macdonaldi:25.484025,Lampanyctus_jordani:25.484025):1.27959):4.501471):6.482136):2.078994):6.087317):5.783799,((Notoscopelus_caudispinosus_resplendens:34.855362,(Gymnoscopelus_nicholsi:16.628589,(Gymnoscopelus_opisthopterus:4.496984,Gymnoscopelus_braueri:4.496984):12.131605):18.226773):10.019237,((Diaphus_sp:15.207586,(Symbolophorus_californiensis:10.112905,Diaphus_rafinesquii:10.112905):5.094681):25.47779,((Electrona_antarctica:14.428311,(Protomyctophum_choriodon:3.104448,Krefftichthys_anderssoni:3.104448):11.323863):15.182154,(Benthosema_glaciale:28.308863,(Myctophum_punctatum:26.445526,((Tarletonbeania_crenularis:21.421451,Symbolophorus_evermanni:21.421451):2.82265,(Hygophum_hygomii:16.998146,Hygophum_proximum:16.998146):7.245955):2.201425):1.863337):1.301602):11.074911):4.189223):6.822733):21.902668)Myctophiformes:99.5,(((Lophotus_lacepede:81.7,(Lampris_guttatus:65.554566,((Regalecus_russelii:12.163691,Regalecus_glesne:12.163691):25.521954,(Desmodema_polystictum:29.911651,(Zu_cristatus:24.186495,(Trachipterus_trachypterus:0.7242,Trachipterus_arcticus:0.7242):23.462295):5.725156):7.773994):27.868921):16.145434)Lampridiformes:68.6,(((Percopsis_transmontana:14.617956,Percopsis_omiscomaycus:14.617956):48.582044,(Aphredoderus_sayanus:41.5,(Speoplatyrhinus_poulsoni:10.886201,(Chologaster_cornuta:10.2227,Troglichthys_rosae:10.2227):0.663501):30.613799):21.7)Percopsiformes:71.791036,((Cyttomimus_affinis:66.46081,(Cyttopsis_rosea:49.2,(Zenopsis_conchifer:33.5,Zeus_faber:33.5):15.7):17.26081)Zeiformes:40.63919,(Stylephorus_chordatus:78.8,((Merluccius_bilinearis:4.814876,Merluccius_productus:4.814876):40.84028,(((Gadomus_dispar:9.947709,Bathygadus_favosus:9.947709):28.939232,(Steindachneria_argentea:35.929201,((Malacocephalus_laevis:17.761913,(Trachonurus_sulcatus:15.56595,(Nezumia_liolepis:6.541893,(Nezumia_bairdii:2.978829,Nezumia_aequalis:2.978829):3.563064):9.024057):2.195963):10.126442,(Macrourus_sp:21.899459,((Coelorinchus_caribbaeus:9.832863,Coelorinchus_caelorhincus:9.832863):12.050918,((Coryphaenoides_armatus:8.705829,Coryphaenoides_rupestris:8.705829):4.710541,(Coryphaenoides_cinereus:4.721775,(Coryphaenoides_acrolepis:1.374281,Albatrossia_pectoralis:1.374281):3.347494):8.694595):8.467411):0.015678):5.988896):8.040846):2.95774):2.613059,((Muraenolepis_marmorata:36.494611,(Physiculus_fulvus:29.55261,((Laemonema_goodebeanorum:2.50946,Laemonema_barbatulum:2.50946):22.579308,(Halargyreus_johnsonii:16.444964,(Lepidion_ensiferus:5.357055,(Antimora_rostrata:0.544543,Antimora_microlepis:0.544543):4.812512):11.087909):8.643804):4.463842):6.942001):1.765507,((Phycis_chesteri:8.038659,(Urophycis_tenuis:5.240437,(Urophycis_regia:4.089467,Urophycis_chuss:4.089467):1.15097):2.798222):25.809917,((Enchelyopus_cimbrius:12.351856,(Gaidropsarus_ensis:1.063842,Gaidropsarus_argentatus:1.063842):11.288014):17.448721,(Lota_lota:23.935378,(Micromesistius_poutassou:16.109498,((Gadus_chalcogrammus:10.882127,Microgadus_proximus:10.882127):0.783593,(Pollachius_virens:7.113828,((Melanogrammus_aeglefinus:4.86848,Merlangius_merlangus:4.86848):0.835458,(Gadus_morhua:3.387041,Gadus_ogac:3.387041):2.316897):1.40989):4.551892):4.443778):7.82588):5.865199):4.047999):4.411542):3.239882):4.155156)Gadiformes:33.144844)Gadariae:28.3)Zeiogadaria:27.891036)Paracanthomorphacea:15.308964):11.083092,((Polymixia_japonica:13.716067,Polymixia_lowei:13.716067)Polymixiiformes:141.083933,((((Diretmus_argenteus:19.059513,Diretmichthys_parini:19.059513):34.941385,((Monocentris_japonica:27.989531,Anomalops_katoptron:27.989531):5.610469,((Hoplostethus_occidentalis_atlanticus:24.361642,Gephyroberyx_darwinii:24.361642):7.918771,(Anoplogaster_cornuta:31.227875,(Paratrachichthys_sajademalensis:17.556284,Aulotrachichthys_prosthemius:17.556284):13.671591):1.052538):1.319587):20.400898):71.278167,(((Beryx_decadactylus:27.236685,Centroberyx_druzhinini:27.236685):43.380061,((Poromitra_crassiceps:24.92187,Scopeloberyx_sp:24.92187):14.219431,(Scopelogadus_beanii:32.606123,(Melamphaes_suborbitalis:16.3971,Melamphaes_lugubris_polylepis:16.3971):16.209023):6.535178):31.475445):40.297009,(((Rondeletia_bicolor:18.618697,Rondeletia_loricata:18.618697):36.665959,(Barbourisia_rufa:46.226385,Acanthochaenus_luetkenii:46.226385):9.058271):34.605995,(Cetostoma_regani:55.49634,(Gyrinomimus_bruuni:21.253796,(Cetomimus_craneae:10.538682,(Gyrinomimus_parri_sp:6.885037,Cetomimus_sp:6.885037):3.653645):10.715114):34.242544):34.394311):21.023104):14.36531)Beryciformes:21.1846,((((Ostichthys_trachypoma:25.197942,(Plectrypops_lima:11.854458,Plectrypops_retrospinis:11.854458):13.343484):5.908719,((Myripristis_murdjan:6.23309,Myripristis_violacea:6.23309):7.08274,(Myripristis_vittata:7.901223,(Myripristis_hexagona:5.776899,Myripristis_berndti:5.776899):2.124324):5.414607):17.790831):21.393339,((Sargocentron_diadema:25.435851,(Holocentrus_rufus:20.788943,(Sargocentron_caudimaculatum:7.933452,Sargocentron_tiere:7.933452):12.855491):4.646908):3.038179,(Sargocentron_cornutum:24.250917,(Neoniphon_marianus:21.359673,(Sargocentron_coruscum:18.908724,(Sargocentron_vexillarium:15.375325,(Neoniphon_argenteus:9.482813,(Neoniphon_opercularis:7.311804,Neoniphon_sammara:7.311804):2.171009):5.892512):3.533399):2.450949):2.891244):4.223113):24.02597)Holocentriformes:92.5,((((Diancistrus_sp:6.205133,Dinematichthys_iluocoeteoides:6.205133):35.622423,(Brosmophycis_marginata:28.531275,((Bidenichthys_capensis:20.411323,(Cataetyx_rubrirostris_lepidogenys:19.611923,Barathronus_maculatus:19.611923):0.7994):2.21586,(Brosmophyciops_pautzkei:16.329087,(Diplacanthopoma_brunnea:8.885971,Diplacanthopoma_brachysoma:8.885971):7.443116):6.298096):5.904092):13.296281):33.572444,((Brotula_barbata:17.13037,Brotula_multibarbata:17.13037):49.097347,(Petrotyx_sanguineus:56.148577,((Bassogigas_gillii:46.424594,(Carapus_bermudensis:36.660247,(Pyramodon_ventralis:4.466651,Onuxodon_parvibrachium:4.466651):32.193596):9.764347):3.154399,((Lamprogrammus_niger:29.409604,(Brotulotaenia_crassa:2.054745,Brotulotaenia_nigra:2.054745):27.354859):15.269313,(Dicrolene_introniger:43.465872,(Neobythites_gilli:38.843863,((Lepophidium_profundorum:11.854747,(Lepophidium_brevibarbe:9.439783,Lepophidium_jeannae:9.439783):2.414964):11.181996,(Genypterus_blacodes:21.59118,(Chilara_taylori:9.435137,(Ophidion_holbrookii:7.404977,(Ophidion_robinsi:3.816636,Ophidion_josephi:3.816636):3.588341):2.03016):12.156043):1.445563):15.80712):4.622009):1.213045):4.900076):6.569584):10.07914):9.172283)Ophidiiaria:57.4,(((Porichthys_notatus:16.879114,Porichthys_plectrodon:16.879114):22.920886,(Batrachoides_pacifici:27.049326,(Sanopus_sp:23.92031,(Opsanus_tau:16.982491,(Opsanus_pardus:4.281706,Opsanus_beta:4.281706):12.700785):6.937819):3.129016):12.750674)Batrachoidaria:87.0,((((Kurtus_indicus:28.882532,Kurtus_gulliveri:28.882532):51.417468,(Pseudamia_gelatinosa:66.307221,(Gymnapogon_urospilotus:39.694196,(Fowleria_aurita:34.463005,((Apogon_campbelli:26.4696,(Cercamia_eremia:23.908259,(Phaeoptyx_pigmentaria:11.611893,(Astrapogon_puncticulatus:0.023741,Astrapogon_stellatus:0.023741):11.588152):12.296366):2.561341):2.957716,(Rhabdamia_cypselura:28.04049,((Nectamia_bandanensis:11.67233,Nectamia_fusca:11.67233):13.919677,((Pristiapogon_exostigma:17.0033,Sphaeramia_orbicularis:17.0033):3.673746,((Ostorhinchus_cookii:15.106505,Cheilodipterus_isostigmus:15.106505):1.061854,((Pterapogon_kauderni:14.744372,Archamia_biguttata:14.744372):0.718897,(Ostorhinchus_lateralis:13.931253,Cheilodipterus_quinquelineatus:13.931253):1.532016):0.70509):4.508687):4.914961):2.448483):1.386826):5.035689):5.231191):26.613025):13.992779)Kurtiformes:22.0,((Odontobutis_potamophila:18.184092,Perccottus_glenii:18.184092):54.615908,(((Oxyeleotris_selheimi:21.63371,Ophiocara_porocephala:21.63371):32.446537,(Dormitator_maculatus:35.276288,Eleotris_acanthopoma_pisonis:35.276288):18.803959):10.350561,(((Gnatholepis_anjerensis:38.174501,Periophthalmus_kalolo:38.174501):5.889022,(Lepidogobius_lepidus:35.790997,(Ctenogobius_boleosoma:21.284121,(Gnatholepis_cauerensis:19.128476,Evorthodus_lyricus:19.128476):2.155645):14.506876):8.272526):10.736043,((Bathygobius_mystacium:40.060582,(Psammogobius_biocellatus:33.064552,(Stonogobiops_nematodes:29.430355,Amblygobius_decussatus:29.430355):3.634197):6.99603):7.789401,((Bollmannia_communis:41.827351,(Gobiosoma_bosc:24.842103,(Elacatinus_oceanops:15.835871,Risor_ruber:15.835871):9.006232):16.985248):3.803827,((Amblygobius_phalaena:33.852188,(Valenciennea_strigata:22.658599,Valenciennea_puellaris:22.658599):11.193589):8.455677,((((Priolepis_cincta:12.807478,Priolepis_hipoliti:12.807478):19.559227,(Lythrypnus_dalli:24.235618,(Trimma_caesiura:11.648806,(Trimma_haima:8.862346,Trimma_okinawae:8.862346):2.78646):12.586812):8.131087):6.799021,((Caffrogobius_caffer:10.837216,Caffrogobius_saldanha:10.837216):27.627397,(Nemateleotris_magnifica:33.001354,((Ptereleotris_evides:7.869852,Ptereleotris_microlepis:7.869852):18.155539,(Gunnellichthys_monostigma:19.574658,(Microdesmus_longipinnis:6.493844,(Cerdale_floridana:5.519568,Microdesmus_bahianus:5.519568):0.974276):13.080814):6.450733):6.975963):5.463259):0.701113):2.082215,(((Eviota_prasites:32.528128,((Paragobiodon_modestus:13.283374,Gobiodon_quinquestrigatus:13.283374):11.589105,(Eviota_saipanensis:17.071894,Eviota_albolineata:17.071894):7.800585):7.655649):5.201852,(Cryptocentrus_sp:25.671245,((Istigobius_ornatus:4.615259,Istigobius_decoratus:4.615259):16.848541,(Cabillus_lacertops:17.846145,Oplopomus_oplopomus:17.846145):3.617655):4.207445):12.058735):1.491938,((Asterropteryx_semipunctata:25.325187,((Amblyeleotris_guttata:7.864651,Amblyeleotris_wheeleri:7.864651):9.151658,(Ctenogobiops_crocineus:16.005212,(Vanderhorstia_ornatissima:14.387222,Amblyeleotris_gymnocephala:14.387222):1.61799):1.011097):8.308878):7.098031,((Fusigobius_inframaculatus:12.952571,Fusigobius_duospilus:12.952571):7.233616,(Fusigobius_neophytus:17.505252,(Lophogobius_cyprinoides:10.250335,(Coryphopterus_glaucofraenum:7.46654,Coryphopterus_personatus:7.46654):2.783795):7.254917):2.680935):12.237031):6.7987):2.026023):1.059924):3.323313):2.218805):6.949583):9.631242):8.369192)Gobiiformes:29.5)Gobiaria:19.3,(((((Dactylopterus_volitans:20.458186,(Dactyloptena_orientalis:7.214807,(Dactyloptena_gilberti:2.919428,Dactyloptena_peterseni:2.919428):4.295379):13.243379):47.664285,((Aulostomus_maculatus:3.200001,Aulostomus_chinensis:3.200001):57.239989,(Aeoliscus_strigatus:43.600001,(Macroramphosus_gracilis:5.883933,Macroramphosus_scolopax:5.883933):37.716068):16.839989):7.682481):6.177529,(((Fistularia_petimba:7.204972,Fistularia_commersonii:7.204972):58.259045,((Mullus_auratus:24.577143,(Upeneus_parvus:19.179076,Upeneus_moluccensis:19.179076):5.398067):2.672626,(Mulloidichthys_flavolineatus:25.441465,(Pseudupeneus_maculatus:15.979258,(Parupeneus_trifasciatus:4.100579,(Parupeneus_barberinus:3.38916,Parupeneus_ciliatus:3.38916):0.711419):11.878679):9.462207):1.808304):38.214248):6.268813,((Callionymus_sp_bairdi:30.894226,((Synchiropus_agassizii:0.851781,Foetorepus_sp:0.851781):24.873888,(Diplogrammus_goramensis:17.442815,(Synchiropus_splendidus:14.508638,(Synchiropus_stellatus:8.137653,Neosynchiropus_ocellatus:8.137653):6.370985):2.934177):8.282854):5.168557):38.260889,(Eurypegasus_draconis:65.64311,(Doryrhamphus_excisus:39.599999,((Corythoichthys_intestinalis:2.629327,Corythoichthys_schultzi:2.629327):33.028171,(Hippocampus_erectus:25.989236,(Syngnathus_leptorhynchus:7.074912,(Syngnathus_louisianae:4.827918,(Syngnathus_scovelli:4.580336,Syngnathus_fuscus:4.580336):0.247582):2.246994):18.914324):9.668262):3.942501):26.043111):3.512005):2.577715):2.56717)Syngnatharia:20.27,((Scomber_japonicus:4.292969,Scomber_scombrus:4.292969):45.965904,((Chiasmodon_sp:36.884665,(Kali_indica:28.600878,(Chiasmodon_niger:14.522577,Kali_kerberti:14.522577):14.078301):8.283787):7.015335,((Icichthys_lockingtoni:34.372462,Pomatomus_saltatrix:34.372462):6.93403,((((Ariomma_bondi:12.831791,Ariomma_melanum:12.831791):12.813877,(Psenes_cyanophrys:20.264382,((Psenes_maculatus:15.780543,Cubiceps_baxteri:15.780543):3.303857,(Cubiceps_gracilis:18.604892,Cubiceps_pauciradiatus:18.604892):0.479508):1.179982):5.381286):5.370387,(Gymnosarda_unicolor:26.302684,((Sarda_sarda:18.215903,(Acanthocybium_solandri:14.420752,(Scomberomorus_regalis_commerson:7.842592,Scomberomorus_maculatus_sp:7.842592):6.57816):3.795151):6.759679,(Thunnus_albacares:17.003014,((Euthynnus_alletteratus:3.751817,Euthynnus_affinis:3.751817):7.215584,(Auxis_rochei:9.033975,Katsuwonus_pelamis:9.033975):1.933426):6.035613):7.972568):1.327102):4.713371):6.343743,(((Peprilus_paru:10.110058,(Peprilus_simillimus:7.302727,(Peprilus_burti:2.50774,Peprilus_triacanthus:2.50774):4.794987):2.807331):25.494483,(Paradiplospinus_gracilis:31.501244,((Brama_brama:13.66353,Brama_japonica:13.66353):4.217393,((Taractichthys_longipinnis:11.841336,Taractes_asper:11.841336):4.735164,(Pteraclis_aesticola:12.131925,Pterycombus_brama:12.131925):4.444575):1.304423):13.620321):4.103297):0.296023,((Scombrolabrax_heterolepis:28.761027,(Icosteus_aenigmaticus:25.018175,(Caristius_sp:6.968809,(Caristius_macropus:4.190999,Platyberyx_opalescens:4.190999):2.77781):18.049366):3.742852):5.213053,((Ruvettus_pretiosus:29.901671,((Neoepinnula_americana:7.819861,Neoepinnula_orientalis:7.819861):20.15755,(Gempylus_serpens:25.446041,Nealotus_tripes:25.446041):2.53137):1.92426):2.413423,(Benthodesmus_simonyi:22.609385,(Aphanopus_carbo:21.676014,(Lepidopus_altifrons:19.481106,(Assurger_anzac:17.367706,(Trichiurus_lepturus:15.1992,Evoxymetopon_taeniatus:15.1992):2.168506):2.1134):2.194908):0.933371):9.705709):1.658986):1.926484):1.459234):3.946694):2.593508):6.358873)Pelagiaria:44.311127):21.920866,((((((Monopterus_albus:69.152565,(Indostomus_paradoxus:2.692657,Indostomus_crocodilus:2.692657):66.459908):4.547573,(Macrognathus_siamensis:18.064552,(Mastacembelus_erythrotaenia:7.602283,(Mastacembelus_niger:7.070436,(Mastacembelus_brachyrhinus:2.807681,Mastacembelus_cunningtoni:2.807681):4.262755):0.531847):10.462269):55.635586)Synbranchiformes:6.999862,(((Ctenopoma_kingsleyae:33.074312,Microctenopoma_nanum:33.074312):29.724657,((Trichopodus_pectoralis:45.626493,Betta_splendens:45.626493):14.077746,Helostoma_temminkii:59.704239):3.09473):7.867293,((Channa_lucius:35.481445,(Channa_striata:16.235812,Channa_melasoma:16.235812):19.245633):31.96482,((Pristolepis_sp:14.79164,Pristolepis_fasciata:14.79164):48.798177,((Dario_dario:38.556398,Badis_pyema:38.556398):6.970876,(Nandus_nebulosus:12.970614,(Nandus_andrewi:1.360622,Nandus_nandus:1.360622):11.609992):32.55666):18.062543):3.856448):3.219997)Anabantiformes:10.033738)Anabantaria:15.7,((Nematistius_pectoralis:60.09561,((Coryphaena_hippurus:19.129261,Rachycentron_canadum:19.129261):12.770739,(Remora_osteochir_australis:10.181739,(Phtheirichthys_lineatus:1.848715,(Echeneis_naucrates:0.500665,Echeneis_neucratoides:0.500665):1.34805):8.333024):21.718261):28.19561)Carangiformes:9.30439,((((Sphyraena_putnamae:18.204293,(Sphyraena_jello:10.332121,Sphyraena_barracuda:10.332121):7.872172):20.141759,(Sphyraena_japonica:20.644035,(Sphyraena_sphyraena:13.957629,Sphyraena_argentea:13.957629):6.686406):17.702017):27.571991,(Mene_maculata:60.366767,(Leptomelanosoma_indicum:17.701093,((Polydactylus_octonemus:1.175876,Polydactylus_virginicus:1.175876):15.036527,(Polydactylus_sextarius:14.030604,(Eleutheronema_rhadinum:4.364669,Eleutheronema_tetradactylum:4.364669):9.665935):2.181799):1.48869):42.665674):5.551276):2.881957,((((Leptobrama_muelleri:46.74854,(Toxotes_jaculatrix:5.197436,Toxotes_chatareus:5.197436):41.551104):5.100583,(Xiphias_gladius:27.944272,(Kajikia_albida:5.679945,((Makaira_sp:0.432391,Makaira_nigricans:0.432391):4.487487,(Istiophorus_platypterus:4.068899,Tetrapturus_angustirostris:4.068899):0.850979):0.760067):22.264327)Istiophoriformes:23.904851):5.268959,(((Scomberoides_lysan:21.219545,Oligoplites_saurus:21.219545):17.792734,(Trachinotus_ovatus:13.314295,(Trachinotus_carolinus:9.406599,Trachinotus_falcatus:9.406599):3.907696):25.697984):13.258708,((Elagatis_bipinnulata:37.121685,(Seriola_rivoliana:2.736423,Seriola_dumerili:2.736423):34.385262):12.878315,((Selar_crumenophthalmus:19.039156,(Trachurus_lathami:14.233199,(Decapterus_macarellus:9.835702,Decapterus_punctatus:9.835702):4.397497):4.805957):10.815977,(((Uraspis_secunda:12.59363,Carangoides_ferdau:12.59363):4.431692,(Carangoides_plagiotaenia:14.464621,(Alectis_ciliaris:12.400521,(Selene_setapinnis:4.199124,Selene_brownii:4.199124):8.201397):2.0641):2.560701):8.762253,((Atule_mate:19.595354,Gnathanodon_speciosus:19.595354):2.99285,((Chloroscombrus_chrysurus:16.12094,Hemicaranx_amblyrhynchus:16.12094):4.09982,(Caranx_crysos_ruber:11.659237,(Caranx_ignobilis:5.894184,Caranx_sexfasciatus:5.894184):5.765053):8.561523):2.367444):3.199371):4.067558):20.144867):2.270987)Carangiformes:4.847095):4.483123,((Psettodes_erumei:11.554984,Psettodes_belcheri:11.554984)Pleuronectiformes:47.878181,(((Centropomus_undecimalis:18.591092,(Centropomus_viridis:11.439461,(Centropomus_ensiferus:9.747409,Centropomus_medius:9.747409):1.692052):7.151631):33.308908,(Psammoperca_waigiensis:32.050648,(Lates_calcarifer:12.768362,(Lates_japonicus:9.697422,Lates_microlepis:9.697422):3.07094):19.282286):19.849352):6.052595,((Lepidoblepharon_ophthalmolepis:41.293483,(Citharoides_macrolepis:16.362693,Citharus_linguatula:16.362693):24.93079):12.306517,(((Trinectes_maculatus:21.130154,((Hypoclinemus_sp:13.017378,Achirus_lineatus:13.017378):4.716285,(Gymnachirus_texae:0.95788,Gymnachirus_melas:0.95788):16.775783):3.396491):29.434162,((Plagiopsetta_glossa:10.222577,(Samariscus_xenicus:5.445401,(Samariscus_latus:1.431842,Samariscus_japonicus:1.431842):4.013559):4.777176):38.678555,((Poecilopsetta_plinthus:1.380407,Poecilopsetta_beanii:1.380407):44.414968,((Cynoglossus_interruptus:37.589307,(Symphurus_atricaudus:14.112178,(Symphurus_civitatium:4.483656,Symphurus_plagiusa:4.483656):9.628522):23.477129):4.810693,((Aseraggodes_heemstrai:16.814795,Aseraggodes_kobensis:16.814795):15.728788,((Microchirus_frechkopi:13.571956,(Solea_solea:8.376781,Pegusa_lascaris:8.376781):5.195175):11.420474,(Heteromycteris_japonicus:21.514274,(Brachirus_annularis:9.83189,(Pseudaesopia_japonica:4.329537,Soleichthys_heterorhinos:4.329537):5.502353):11.682384):3.478156):7.551153):9.856417):3.395375):3.105757):1.663184):1.527715,(((Scophthalmus_maximus:28.781036,(Scophthalmus_aquosus:23.377292,Lepidorhombus_boscii:23.377292):5.403744):17.657396,(Oncopterus_darwinii:33.462802,((Mancopsetta_maculata:0.642821,Neoachiropsetta_milfordi:0.642821):21.848025,(Rhombosolea_leporina:4.689959,(Rhombosolea_tapirina:1.43641,Rhombosolea_plebeia:1.43641):3.253549):17.800887):10.971956):12.97563):3.872127,(((Paralichthys_dentatus:34.43969,((Cyclopsetta_chittendeni:12.257242,Syacium_micrurum:12.257242):18.779966,(Citharichthys_sordidus:17.474326,(Citharichthys_arctifrons:14.706003,(Etropus_crossotus:11.508059,Etropus_microstomus:11.508059):3.197944):2.768323):13.562882):3.402482):6.355634,(Laeops_kitaharae:18.800001,(Chascanopsetta_lugubris:17.9796,((Bothus_lunatus:13.322564,Bothus_robinsi:13.322564):4.413016,((Monolene_sp:14.104021,Trichopsetta_ventralis:14.104021):2.837074,(Asterorhombus_cocosensis:15.876155,(Psettina_tosana:12.742948,(Arnoglossus_blachei:6.90431,Arnoglossus_imperialis:6.90431):5.838638):3.133207):1.06494):0.794485):0.24402):0.820401):21.995323):4.386767,((Xystreurys_liolepis:17.395832,(Pseudorhombus_pentophthalmus:16.378967,((Gastropsetta_frontalis:3.26495,Ancylopsetta_ommata:3.26495):8.785002,(Paralichthys_californicus:6.786751,Paralichthys_albigutta:6.786751):5.263201):4.329015):1.016865):4.08644,(Atheresthes_evermanni:19.686963,(Hypsopsetta_guttulata:17.244973,(((Glyptocephalus_zachirus:5.117694,(Embassichthys_bathybius:3.72555,Microstomus_pacificus:3.72555):1.392144):2.549352,(Lyopsetta_exilis:5.963901,(Hippoglossus_hippoglossus:5.106949,Eopsetta_jordani:5.106949):0.856952):1.703145):2.223697,((Limanda_limanda:4.588583,Hippoglossoides_elassodon:4.588583):3.218528,(Pseudopleuronectes_americanus:6.96439,((Platichthys_stellatus:3.732552,Pleuronectes_platessa:3.732552):2.370544,(Parophrys_vetulus:4.449471,(Lepidopsetta_bilineata:4.099454,(Isopsetta_isolepis:3.813873,Psettichthys_melanostictus:3.813873):0.285581):0.350017):1.653625):0.861294):0.842721):2.083632):7.35423):2.44199):1.795309):23.699819):5.128468):1.781472):1.507969)Pleuronectiformes:4.352595):1.48057):2.16804):7.198795):0.6)Carangiaria:27.0):12.050153,((((Polycentropsis_abbreviata:46.103084,(Monocirrhus_polyacanthus:27.472033,Polycentrus_schomburgkii:27.472033):18.631051):48.114875,(Pholidichthys_leucotaenia:88.7,((Etroplus_maculatus:49.297945,Paretroplus_maculatus:49.297945):27.102055,((Paratilapia_polleni:48.325588,Ptychochromis_grandidieri:48.325588):20.810997,((Cichla_temensis:52.934446,(Crenicichla_lepidota:50.100001,(Herichthys_cyanoguttatus:23.172861,(Symphysodon_discus:17.001924,Heros_efasciatus:17.001924):6.170937):26.92714):2.834445):8.965484,(Heterochromis_multidens:57.250288,(Nanochromis_parilus:29.79536,(Oreochromis_niloticus:18.346974,(Tilapia_louka:15.389183,(Steatocranus_gibbiceps:12.134063,(Neolamprologus_brichardi:9.183198,(Astatotilapia_burtoni:4.073468,(Pundamilia_nyererei:2.748366,Maylandia_zebra:2.748366):1.325102):5.10973):2.950865):3.25512):2.957791):11.448386):27.454928):4.649642):7.236655):7.263415)Cichliformes:12.3)Cichlomorphae:5.517959):0.428115,((((Atherinopsis_californiensis:20.110119,((Odontesthes_argentinensis:3.243131,Odontesthes_humensis:3.243131):4.430301,(Odontesthes_retropinnis:1.282477,Odontesthes_bonariensis:1.282477):6.390955):12.436687):28.607397,(Membras_martinica:26.507117,(Labidesthes_sicculus:14.034561,((Poblana_ferdebueni:5.445417,Menidia_beryllina:5.445417):1.240313,(Menidia_menidia:5.800579,Menidia_peninsulae:5.800579):0.885151):7.348831):12.472556):22.210399):22.224664,(Iso_sp:49.320038,(Rheocles_wrightae:45.587422,((Craterocephalus_honoriae:40.343535,(Atherinomorus_stipes:27.417921,(Atherinomorus_lacunosus:18.10875,Atherinomorus_vaigiensis:18.10875):9.309171):12.925614):3.445895,((Rhadinocentrus_ornatus:23.847475,(Melanotaenia_splendida:10.116474,(Melanotaenia_sp:6.026677,Melanotaenia_trifasciata:6.026677):4.089797):13.731001):16.025407,(Marosatherina_ladigesi:33.738999,(Phenacostethus_smithi:27.920636,(Pseudomugil_gertrudae:17.876274,Pseudomugil_signifer:17.876274):10.044362):5.818363):6.133883):3.916548):1.797992):3.732616):21.622142)Atheriniformes:6.45782,((Pachypanchax_playfairii:66.88735,((Poecilia_latipinna_reticulata:14.292785,(Poeciliopsis_elongata:12.312835,(Heterandria_formosa:11.367362,(Gambusia_affinis:5.73674,Belonesox_belizanus:5.73674):5.630622):0.945473):1.97995):30.131968,((Floridichthys_carpio:20.456976,(Cyprinodon_variegatus:13.822603,Jordanella_floridae:13.822603):6.634373):20.014113,(Fundulus_parvipinnis:18.797065,((Fundulus_heteroclitus:12.933656,Lucania_parva_goodei:12.933656):1.1775,(Adinia_xenica:11.46608,(Fundulus_blairae:10.804496,Fundulus_chrysotus:10.804496):0.661584):2.645076):4.685909):21.674024):3.953664):22.462597)Cyprinodontiformes:9.514255,(Oryzias_latipes:71.879041,((Zenarchopterus_dispar:32.763495,(Dermogenys_collettei:29.885486,((Xenentodon_cancila:17.254219,(Tylosurus_crocodilus:6.568468,Ablennes_hians:6.568468):10.685751):6.744727,(Strongylura_notata:20.277008,(Platybelone_argalus:18.768659,(Cololabis_saira:2.646874,Scomberesox_saurus:2.646874):16.121785):1.508349):3.721938):5.88654):2.878009):14.301133,((Arrhamphus_sclerolepis:24.704904,(Hyporhamphus_affinis:1.178428,Hyporhamphus_dussumieri:1.178428):23.526476):12.189109,((Hemiramphus_brasiliensis:13.392495,Oxyporhamphus_micropterus:13.392495):10.26042,(Parexocoetus_brachypterus:18.641912,((Cypselurus_callopterus:6.414034,Exocoetus_monocirrhus:6.414034):4.606228,((Cheilopogon_pinnatibarbatus:8.078435,Cheilopogon_melanurus:8.078435):1.264667,(Hirundichthys_marginatus:7.633585,(Cheilopogon_dorsomacula:3.938268,Prognichthys_brevipinnis:3.938268):3.695317):1.709517):1.67716):7.62165):5.011003):13.241098):10.170615):24.814413)Beloniformes:4.522564):0.998395)Atherinomorphae:17.246074):2.573621,(((Parambassis_ranga:4.300467,Ambassis_urotaenia:4.300467):42.908908,(Ambassis_agrammus:37.721223,Ambassis_interrupta:37.721223):9.488152):47.378136,(((Halidesmus_scapularis:19.129654,(Congrogadus_subducens:12.423811,Natalichthys_sam:12.423811):6.705843):65.72699,((Parma_microlepis:29.067354,(((Plectroglyphidodon_johnstonianus:8.386886,Plectroglyphidodon_dickii:8.386886):9.65747,(Hypsypops_rubicundus:12.304306,(Microspathodon_chrysurus:6.881828,Microspathodon_bairdii:6.881828):5.422478):5.74005):5.039146,(Stegastes_albifasciatus:21.575703,(Lepidozygus_tapeinosoma:19.961142,(Stegastes_partitus:10.740451,(Stegastes_fuscus:3.606957,Stegastes_diencaeus:3.606957):7.133494):9.220691):1.614561):1.507799):5.983852):6.532645,(((Chromis_atripectoralis:23.92163,(Chromis_cyanea:19.668093,Azurina_hirundo:19.668093):4.253537):2.560879,(Chromis_dimidiata:21.589296,(Dascyllus_aruanus:10.42299,(Dascyllus_carneus:5.674743,(Dascyllus_reticulatus:3.294907,Dascyllus_trimaculatus:3.294907):2.379836):4.748247):11.166306):4.893213):5.996685,((Abudefduf_saxatilis:8.193306,(Abudefduf_vaigiensis:6.153846,Abudefduf_sexfasciatus:6.153846):2.03946):23.164854,(Chrysiptera_taupou:23.043912,((Dischistodus_perspicillatus:16.667977,Pomachromis_richardsoni:16.667977):4.069637,(Amphiprion_ocellaris:19.611053,(((Amblyglyphidodon_leucogaster:14.024721,Acanthochromis_polyacanthus:14.024721):1.281718,(Neoglyphidodon_polyacanthus:11.183065,Neoglyphidodon_melas:11.183065):4.123374):2.967532,((Neopomacentrus_cyanomos:16.106197,Amphiprion_clarkii:16.106197):1.301497,(Pomacentrus_brachialis:11.482593,(Pomacentrus_spilotoceps:10.044386,Pomacentrus_pavo:10.044386):1.438207):5.925101):0.866277):1.337082):1.126561):2.306298):8.314248):1.121034):3.120805):49.256645):8.186887,(((Amphistichus_argenteus:7.3609,Hyperprosopon_anale_argenteum:7.3609):5.12006,(Cymatogaster_aggregata:9.498888,((Embiotoca_jacksoni:4.621261,Embiotoca_lateralis:4.621261):1.152342,(Zalembius_rosaceus:3.479384,(Phanerodon_furcatus:2.729151,Rhacochilus_vacca:2.729151):0.750233):2.294219):3.725285):2.982072):79.054345,((Neomyxus_leuciscus:45.332456,((Mugil_curema:21.429647,(Mugil_cephalus:19.263361,Mugil_trichodon:19.263361):2.166286):15.095634,((Moolgarda_engeli:15.623766,(Valamugil_buchanani:7.258517,Crenimugil_crenilabis:7.258517):8.365249):10.899382,(Myxus_capensis:20.370079,(Liza_richardsonii:11.151445,Chelon_macrolepis:11.151445):9.218634):6.153069):10.002133):8.807175)Mugiliformes:44.431485,((Lipogramma_trilineata:30.399056,Lipogramma_anabantoides:30.399056):57.64089,((Plesiops_coeruleolineatus:7.580044,Plesiops_melas:7.580044):79.404154,((Pseudoplesiops_revellei:60.598835,((Ogilbyina_novaehollandiae:22.700357,Labracinus_cyclophthalmus:22.700357):2.267877,(Pholidochromis_cerasina:20.528889,(Pseudochromis_fridmani:15.807128,(Pseudochromis_jamesi:14.334036,Pseudochromis_cyanotaenia:14.334036):1.473092):4.721761):4.439345):35.630601):25.023364,(Gramma_loreto:81.164935,((Opistognathus_maxillosus:33.277138,(Opistognathus_aurifrons:26.588425,Lonchopisthus_micrognathus:26.588425):6.688713):45.925,((((Lepadichthys_lineatus:17.336596,Diademichthys_lineatus:17.336596):20.225914,(Arcos_sp:18.655154,Gobiesox_maeandricus:18.655154):18.907356):35.987836,((Enneanectes_altivelis:31.556734,Enneanectes_boehlkei:31.556734):24.338998,(Enneapterygius_gruschkai:48.526856,(Enneapterygius_abeli:26.039104,(Helcogramma_ellioti_sp:11.052312,Helcogramma_fuscopinna:11.052312):14.986792):22.487752):7.368876):17.654614):3.123025,(((Gibbonsia_metzi:32.42937,((Pavoclinus_profundus:3.311804,Blennophis_striatus:3.311804):5.261594,(Clinus_cottoides:7.813834,(Clinus_superciliosus:5.776931,Muraenoclinus_dorsalis:5.776931):2.036903):0.759564):23.855972):18.31495,((((Stathmonotus_stahli:34.294766,Paraclinus_marmoratus:34.294766):8.524384,(Platygillellus_rubrocinctus:33.273043,Gillellus_semicinctus:33.273043):9.546107):2.824818,((Acanthemblemaria_paula:10.291854,Acanthemblemaria_aspera:10.291854):11.643632,(Emblemaria_pandionis:16.274634,(Lucayablennius_zingaro:10.917724,Chaenopsis_sp_alepidota:10.917724):5.35691):5.660852):23.708482):2.401714,(Neoclinus_blanchardi:45.65764,((Starksia_atlantica:20.906785,(Starksia_fasciata:15.54431,Starksia_ocellata:15.54431):5.362475):21.54664,((Labrisomus_multiporosus:23.811556,Labrisomus_nigricinctus:23.811556):11.340578,(Labrisomus_bucciferus:30.847081,(Malacoctenus_aurolineatus:19.434339,Malacoctenus_triangulatus:19.434339):11.412742):4.305053):7.301291):3.204215):2.388042):2.698638):17.52193,((Ecsenius_midas:20.757533,(Ecsenius_pardus:9.330095,Ecsenius_opsifrontalis:9.330095):11.427438):26.44987,(((Hypleurochilus_sp:28.590185,Hypsoblennius_hentz:28.590185):8.588366,(Enchelyurus_flavipes:35.153742,(Petroscirtes_mitratus:20.738729,(Meiacanthus_oualanensis_grammistes:18.49006,(Plagiotremus_rhinorhynchos:12.234118,Plagiotremus_tapeinosoma:12.234118):6.255942):2.248669):14.415013):2.024809):6.428789,((Cirripectes_stigmaticus:23.977773,(Ophioblennius_atlanticus:21.259299,(Cirripectes_quagga:16.143896,(Cirripectes_castaneus:12.588225,Cirripectes_filamentosus:12.588225):3.555671):5.115403):2.718474):13.192955,((Stanulus_sp:27.293598,(Alticus_arnoldorum:21.373525,(Nannosalarias_nativitatis:16.616851,(Salarias_fasciatus:4.970758,Atrosalarias_fuscus:4.970758):11.646093):4.756674):5.920073):3.750936,(Praealticus_caesius:21.121348,((Entomacrodus_nigricans:6.651164,(Entomacrodus_striatus:2.935441,Entomacrodus_niuafoouensis:2.935441):3.715723):12.782291,((Blenniella_cyanostigma:1.150842,Blenniella_chrysospilos_paula:1.150842):14.096808,(Ecsenius_bicolor:10.039814,(Istiblennius_dussumieri:5.159784,Blenniella_paula:5.159784):4.88003):5.207836):4.185805):1.687893):9.923186):6.126194):6.436612):3.600063):21.058847):8.407121)Blenniiformes:2.528767):1.962797):4.457264):1.361999):1.055748):1.723995):1.771364):1.508226):1.54398):2.632184)Ovalentaria:11.230458):3.449148,(((Gerres_oyena:31.967153,Eugerres_plumieri:31.967153):13.214677,(Gerres_longirostris:33.538035,(Gerres_cinereus:25.835379,(Ulaema_lefroyi:12.216435,(Eucinostomus_argenteus:8.877131,Eucinostomus_gula:8.877131):3.339304):13.618944):7.702656):11.643795):59.618171,((Champsodon_snyderi:93.628367,((Lachnolaimus_maximus:59.825024,(Haletta_semifasciata:53.314716,(Decodon_puellaris:42.908596,(Clepticus_parrae:33.343855,(Bodianus_mesothorax:11.194671,Bodianus_axillaris:11.194671):22.149184):9.564741):10.40612):6.510308):16.825549,(((Novaculichthys_taeniourus:25.653416,Xyrichtys_novacula_martinicensis:25.653416):31.457367,(Cheilio_inermis:53.277111,((Stethojulis_balteata:9.983011,Stethojulis_strigiventer:9.983011):28.997049,((Hologymnosus_doliatus:21.754371,(Coris_caudimacula:15.91273,(Coris_gaimard:8.042665,Coris_formosa:8.042665):7.870065):5.841641):12.40746,(Anampses_lineatus:32.174586,(((Halichoeres_bathyphilus_bivittatus:17.045337,Oxyjulis_californica:17.045337):10.479954,((Labropsis_australis:6.534163,Diproctacanthus_xanthurus:6.534163):12.166505,(Labrichthys_unilineatus:16.11964,Labroides_dimidiatus:16.11964):2.581028):8.824623):1.889232,((Thalassoma_quinquevittatum:7.827371,(Gomphosus_varius:5.806934,(Thalassoma_lunare:3.528429,Thalassoma_amblycephalum:3.528429):2.278505):2.020437):19.363015,((Coris_batuensis:9.160764,Halichoeres_margaritaceus:9.160764):10.736811,(Macropharyngodon_bipartitus:19.739067,(Halichoeres_biocellatus:8.937511,Halichoeres_iridis:8.937511):10.801556):0.158508):7.292811):2.224137):2.760063):1.987245):4.818229):14.297051):3.833672):12.229296,((Pteragogus_enneacanthus:50.69613,((Cirrhilabrus_punctatus:8.392353,Cirrhilabrus_katherinae:8.392353):34.405461,(Pseudocheilinus_evanidus:27.752423,Pseudocheilinus_hexataenia:27.752423):15.045391):7.898316):16.356272,((Tautoga_onitis:13.055908,Tautogolabrus_adspersus:13.055908):48.597667,(((Cheilinus_chlorourus:8.409669,Cheilinus_oxycephalus:8.409669):16.243577,(Epibulus_insidiator:21.250317,((Cheilinus_fasciatus:14.720749,Wetmorella_nigropinnata:14.720749):1.353183,(Oxycheilinus_celebicus:10.10906,(Oxycheilinus_digramma:6.555915,Oxycheilinus_unifasciatus:6.555915):3.553145):5.964872):5.176385):3.402929):33.256324,(Calotomus_carolinus:41.935106,(Cryptotomus_roseus:36.557555,(Hipposcarus_longiceps:26.519779,((Leptoscarus_vaigiensis:18.783016,(Sparisoma_aurofrenatum:5.081416,(Sparisoma_viride:2.797865,Sparisoma_chrysopterum:2.797865):2.283551):13.7016):4.368826,(Cetoscarus_bicolor:19.398126,(Chlorurus_sordidus:12.004268,((Scarus_quoyi:6.267289,Scarus_globiceps:6.267289):3.392749,((Scarus_iseri:6.876703,Scarus_rubroviolaceus:6.876703):1.069357,(Scarus_niger:7.190229,(Chlorurus_gibbus:5.467856,Scarus_ghobban:5.467856):1.722373):0.755831):1.713978):2.34423):7.393858):3.753716):3.367937):10.037776):5.377551):15.974464):3.744005):5.398827):2.287677):7.310494)Labriformes:16.977794):2.671634,((((Drepane_punctata:67.659163,(Chaetodipterus_faber:32.17985,(Platax_orbicularis:9.449899,Platax_teira:9.449899):22.729951):35.479313)Ephippiformes:20.887791,(Dicentrarchus_labrax:22.857155,(Morone_saxatilis:11.716263,(Morone_chrysops:10.272233,(Morone_mississippiensis:6.345988,Morone_americana:6.345988):3.926245):1.44403):11.140892):65.689799):5.265504,((((Datnioides_microlepis:21.631947,Lobotes_surinamensis:21.631947):64.806165,((Menticirrhus_undulatus_littoralis:8.847711,Menticirrhus_saxatilis:8.847711):22.317433,(Leiostomus_xanthurus:27.172082,(Aplodinotus_grunniens:26.095556,((Micropogonias_undulatus:17.304015,Sciaenops_ocellatus:17.304015):7.946327,(Pogonias_cromis:24.82357,((Atractoscion_nobilis:15.728504,(Cynoscion_regalis:4.188845,Cynoscion_arenarius:4.18884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us_spinus:19.354818,(Siganus_argenteus:15.111025,(Siganus_vulpinus:4.808076,(Siganus_stellatus:2.106997,Siganus_punctatus:2.106997):2.701079):10.302949):4.243793):65.776064,(((Scatophagus_argus:14.457935,Selenotoca_multifasciata:14.457935):61.402524,((Cepola_schlegelii:20.839671,Sphenanthias_tosaensis:20.839671):45.661543,(Pristigenys_alta:35.954641,(Priacanthus_arenatus:17.701916,Heteropriacanthus_cruentatus:17.701916):18.252725):30.546573):9.359245):5.908442,((Capros_aper:66.802727,(Antigonia_rubescens:10.905702,Antigonia_capros:10.905702):55.897025):13.997274,(((Lophiodes_reticulatus:22.462201,(Lophius_gastrophysus:2.495452,Lophius_americanus:2.495452):19.966749):42.032117,((Fowlerichthys_radiosus:30.458137,(Histiophryne_cryptacanthus:27.013454,(Histrio_histrio:12.333108,(Antennatus_coccineus:10.534045,Antennatus_nummifer:10.534045):1.799063):14.680346):3.444683):15.341864,((Halieutichthys_aculeatus:21.203888,(Dibranchus_tremendus:17.846967,(Ogcocephalus_parvus_nasutus:0.862633,Ogcocephalus_radiatus:0.862633):16.984334):3.356921):23.262122,((Chaunax_suttkusi:5.449484,Chaunax_stigmaeus:5.449484):33.050089,((Gigantactis_sp:14.287816,(Gigantactis_vanhoeffeni:6.268163,Gigantactis_ios:6.268163):8.019653):18.623814,((Cryptopsaras_couesii:20.548717,(Ceratias_holboelli:2.995618,Ceratias_sp:2.995618):17.553099):10.41616,((Himantolophus_albinares_sagamius:14.456809,(Melanocetus_murrayi:2.918086,Melanocetus_johnsonii:2.918086):11.538723):9.124163,(Bertella_idiomorpha:16.387383,(Oneirodes_macrosteus:10.164362,(Oneirodes_bulbosus:4.568319,Dolopichthys_sp:4.568319):5.596043):6.223021):7.193589):7.383905):1.946753):5.587943):5.966437):1.333991):18.694317)Lophiiformes:15.895554,((Triodon_macropterus:75.474468,((Triacanthus_biaculeatus:64.492986,(Halimochirurgus_alcocki:21.780217,(Triacanthodes_anomalus:1.062324,Triacanthodes_ethiops:1.062324):20.717893):42.712769):10.123884,((Anoplocapros_lenticularis:9.298842,Aracana_aurita:9.298842):45.501158,(Ostracion_cubicus:40.906398,(Rhinesomus_triqueter:20.731735,Acanthostracion_quadricornis:20.731735):20.174663):13.893602):19.81687):0.857598):2.325533,(((Chilomycterus_schoepfii:12.19839,Diodon_holocanthus:12.19839):43.701611,((Tetractenos_hamiltoni:19.959527,Takifugu_rubripes:19.959527):15.640474,(Lagocephalus_laevigatus:34.623454,((Sphoeroides_nephelus:3.189226,Sphoeroides_maculatus:3.189226):29.531603,((Canthigaster_bennetti:10.228754,(Canthigaster_jactator:7.490666,Canthigaster_valentini:7.490666):2.738088):13.996958,((Arothron_hispidus:6.632535,Arothron_nigropunctatus:6.632535):13.663845,(Tetraodon_miurus:18.197952,(Tetraodon_fluviatilis:0.918738,Tetraodon_nigroviridis:0.918738):17.279214):2.098428):3.929332):8.495117):1.902625):0.976547):20.3):17.334862,((Ranzania_laevis:22.000001,(Mola_mola:9.255334,Masturus_lanceolatus:9.255334):12.744667):46.610273,(((Aluterus_scriptus:24.377014,(Amanses_scopas:11.327068,Cantherhines_pardalis_pullus:11.327068):13.049946):3.216101,(Oxymonacanthus_longirostris:26.823609,(Paraluteres_prionurus:22.166933,(Stephanolepis_hispidus:20.308774,(Pervagor_janthinosoma:15.394884,(Acreichthys_tomentosus:14.512206,Pervagor_nigrolineatus:14.512206):0.882678):4.91389):1.858159):4.656676):0.769506):16.206886,(((Pseudobalistes_flavimarginatus:9.839815,(Xanthichthys_ringens:3.788257,Xanthichthys_auromarginatus:3.788257):6.051558):6.146411,(Balistapus_undulatus:12.458223,(Balistoides_conspicillum:10.763366,(Melichthys_niger:4.645391,Melichthys_indicus:4.645391):6.117975):1.694857):3.528003):3.569786,((Pseudobalistes_fuscus:16.149258,(Balistes_vetula:11.073547,Balistes_capriscus:11.073547):5.075711):2.212859,(Canthidermis_maculata:18.117763,((Sufflamen_fraenatum:5.570154,Abalistes_stellatus:5.570154):12.129847,(Sufflamen_chrysopterum:15.515234,(Rhinecanthus_verrucosus:3.424718,(Rhinecanthus_assasi:2.297794,Rhinecanthus_aculeatus:2.297794):1.126924):12.090516):2.184767):0.417762):0.244354):1.193895):24.243989):24.810273):4.624589):4.565138)Tetraodontiformes:2.589871):0.410129):0.9689):3.361981):5.143044):2.709359):0.829173):1.980895,((Centrogenys_vaigiensis:89.029209,((Astroscopus_ygraecum:45.444573,(Uranoscopus_sulphureus:45.364025,(Kathetostoma_albigutta:6.141349,Kathetostoma_averruncus:6.141349):39.222676):0.080548):38.552254,((Ammodytes_dubius:4.401809,Ammodytes_hexapterus:4.401809):74.183219,(Cheimarrichthys_fosteri:72.832529,(Parapercis_punctulata:20.607195,(Parapercis_hexophtalma:10.938132,Parapercis_clathrata:10.938132):9.669063):52.225334):5.752499):5.411799)Uranoscopiformes:5.032382):6.241731,(((((Epigonus_pandionis:33.002561,Epigonus_telescopus:33.002561):53.144111,((Howella_brodiei:26.984078,Howella_zina:26.984078):55.835149,(Acropoma_japonicum:75.274939,Ostracoberyx_dorygenys:75.274939):7.544288):3.327445):3.497909,((Synagrops_bellus:36.307076,Synagrops_spinosus:36.307076):52.374034,((Malakichthys_elegans:82.997929,(Stereolepis_gigas:77.80727,(Lateolabrax_japonicus:70.780688,Polyprion_americanus:70.780688):7.026582):5.190659):4.901463,((Banjos_banjos:60.576642,(Histiopterus_typus:49.182805,(Pentaceros_japonicus:33.520619,(Pentaceros_wheeleri:31.203915,Pentaceros_pectoralis:31.203915):2.316704):15.662186):11.393837):26.783473,((Acanthaphritis_unoorum:66.166223,Limnichthys_sp:66.166223):18.796719,((Glaucosoma_buergeri:11.362664,Glaucosoma_hebraicum:11.362664):55.254693,(Parapriacanthus_ransonneti:44.085728,((Pempheris_schomburgkii:29.121414,Pempheris_schwenkii:29.121414):2.45015,(Pempheris_vanicolensis:3.428146,Pempheris_oualensis:3.428146):28.143418):12.514164):22.531629):18.345585):2.397173):0.539277):0.781718):0.963471)Pempheriformes:3.529907,((Girella_nigricans_mezina:73.558804,((Oplegnathus_punctatus:61.207262,(Kuhlia_rupestris:21.296641,(Kuhlia_mugil:17.371047,Kuhlia_marginata:17.371047):3.925594):39.910621):7.298334,((Terapon_jarbua:28.825085,(Hephaestus_fuliginosus:7.127721,Scortum_barcoo:7.127721):21.697364):34.976869,(Kyphosus_sectatrix:20.590539,(Kyphosus_incisor:10.664446,(Kyphosus_cinerascens:6.772866,Kyphosus_elegans:6.772866):3.89158):9.926093):43.211415):4.703642):5.053208)Terapontiformes:11.103907,((Macquaria_colonorum:7.18407,Macquaria_novemaculeata:7.18407):68.510836,((Maccullochella_peelii:51.757161,(Gadopsis_marmoratus:50.773244,((Nannoperca_australis:38.168409,Macquaria_ambigua:38.168409):3.948007,(Percichthys_trucha:18.997907,Percilia_irwini:18.997907):23.118509):8.656828):0.983917):17.94284,((((Amblycirrhitus_pinos:35.323278,Paracirrhites_forsteri_arcatus:35.323278):4.393797,(Neocirrhites_armatus:31.535456,(Cirrhitichthys_oxycephalus:20.902936,Cirrhitichthys_falco:20.902936):10.63252):8.181619):26.749986,((Cheilodactylus_fasciatus:22.013875,Cheilodactylus_pixi:22.013875):11.724293,(Cheilodactylus_variegatus:12.963263,(Chirodactylus_jessicalenorum:4.995569,Chirodactylus_brachydactylus:4.995569):7.967694):20.774905):32.728893):2.532124,((Enoplosus_armatus:51.893024,(Coreoperca_whiteheadi:38.15934,(Siniperca_scherzeri:7.973286,Siniperca_chuatsi:7.973286):30.186054):13.733684):11.154204,((Elassoma_okefenokee:9.831207,(Elassoma_evergladei:5.031386,Elassoma_zonatum:5.031386):4.799821):39.268794,(Acantharchus_pomotis:35.569279,((Pomoxis_nigromaculatus:16.7,(Archoplites_interruptus:15.292892,Ambloplites_rupestris:15.292892):1.407108):12.310412,(Micropterus_salmoides:24.739672,(Lepomis_macrochirus:9.083859,Lepomis_cyanellus:9.083859):15.655813):4.27074):6.558867):13.530722):13.947227):5.951957):0.700816):5.994905)Centrarchiformes:8.967805):8.511777):1.725513,(((Centropristis_striata:46.868256,(Paralabrax_nebulifer:37.52673,((Serranus_tigrinus:22.855237,Serranus_baldwini:22.855237):12.480224,(Hypoplectrus_puella:24.888476,((Diplectrum_formosum:0.700106,Diplectrum_bivittatum:0.700106):18.738279,(Serranus_notospilus:5.874997,Serranus_phoebe:5.874997):13.563388):5.450091):10.446985):2.191269):9.341526):33.250855,(((Liopropoma_mowbrayi:8.336871,Liopropoma_rubre:8.336871):59.844566,((Pseudanthias_squamipinnis:27.847937,Pseudanthias_pascalus:27.847937):7.275049,(Odontanthias_chrysostictus:30.856299,(Baldwinella_aureorubens:21.177277,(Baldwinella_vivana:13.154899,(Anthias_nicholsi:8.44807,Pronotogrammus_martinicensis:8.44807):4.706829):8.022378):9.679022):4.266687):33.058451):7.392005,(((Aporops_bilinearis:19.595822,Pseudogramma_polyacantha:19.595822):27.656961,((Rypticus_saponaceus:11.018604,Rypticus_subbifrenatus:11.018604):12.543979,(Grammistops_ocellatus:21.237152,Grammistes_sexlineatus:21.237152):2.325431):23.6902):19.590974,((Hyporthodus_flavolimbatus:17.216026,(Mycteroperca_bonaci_microlepis:14.018424,(Epinephelus_maculatus:9.679715,Epinephelus_merra:9.679715):4.338709):3.197602):13.920868,(Aethaloperca_rogaa:25.497843,(Cephalopholis_argus:20.000404,(Cephalopholis_fulva:14.49995,Cephalopholis_miniata:14.49995):5.500454):5.497439):5.639051):35.706863):8.729685):4.545669):2.08089,((Niphon_spinosus:66.034644,(((Perca_fluviatilis:26.565471,Perca_flavescens:26.565471):6.076088,(Sander_vitreus:20.44789,(Romanichthys_valsanicola:10.653018,(Zingel_zingel:8.54132,Zingel_streber:8.54132):2.111698):9.794872):12.193669):7.620138,((Gymnocephalus_cernuus:17.782765,Gymnocephalus_schraetser:17.782765):10.222622,(((Etheostoma_juliae:17.148898,Etheostoma_vitreum:17.148898):3.259541,(Etheostoma_zonale:14.408119,(Etheostoma_simoterum:1.030301,Etheostoma_atripinne:1.030301):13.377818):6.00032):2.94762,((Percina_caprodes:13.615157,(Percina_phoxocephala:11.718805,Percina_nigrofasciata:11.718805):1.896352):8.422575,(Crystallaria_asprella:18.728111,(Ammocrypta_beanii:10.972819,(Ammocrypta_meridiana:5.304536,Ammocrypta_pellucida:5.304536):5.668283):7.755292):3.309621):1.318327):4.649328):12.25631):25.772947):12.542662,(((Cottoperca_trigloides:32.48141,Bovichtus_diacanthus:32.48141):30.539844,(Pseudaphritis_urvillii:46.262203,(Eleginops_maclovinus:26.692961,(Aethotaxis_mitopteryx:11.515338,(Dissostichus_eleginoides:11.01354,((Patagonotothen_tessellata:6.247258,Pagothenia_borchgrevinki:6.247258):4.476855,(Gobionotothen_gibberifrons:10.30631,(Notothenia_coriiceps:9.671118,((Harpagifer_antarcticus:6.338216,(Artedidraco_orianae:2.348106,Pogonophryne_barsukovi:2.348106):3.99011):1.076471,(Gymnodraco_acuticeps:6.79299,(Parachaenichthys_charcoti:6.390345,(Chionodraco_rastrospinosus:1.867689,Chionobathyscus_dewitti:1.867689):4.522656):0.402645):0.621697):2.256431):0.635192):0.417803):0.289427):0.501798):15.177623):19.569242):16.759051):12.936898,(((Bembras_japonica:49.422473,Parabembras_curtus:49.422473):19.932841,(((Bembrops_gobioides:4.349162,Bembrops_anatirostris:4.349162):58.182241,((Peristedion_ecuadorense:22.894708,(Peristedion_truncatum:9.471985,Peristedion_gracile:9.471985):13.422723):31.638001,(Pterygotrigla_hemisticta:41.909694,(Bellator_militaris:29.437262,(Prionotus_carolinus:18.132099,(Prionotus_evolans:4.835825,Prionotus_stephanophrys:4.835825):13.296274):11.305163):12.472432):12.623015):7.998694):3.954878,((Synanceia_verrucosa:22.624589,Coccotropsis_gymnoderma:22.624589):39.886512,((Scorpaenodes_guamensis:26.552475,(Scorpaenodes_albaiensis:24.974821,((Pterois_antennata:7.017601,Pterois_radiata:7.017601):0.638804,(Dendrochirus_zebra:5.919494,Pterois_miles:5.919494):1.736911):17.318416):1.577654):19.705166,(((Sebastolobus_alascanus:4.444486,Adelosebastes_latens:4.444486):30.466055,(Helicolenus_dactylopterus:15.754405,((Sebastes_paucispinis:9.408429,Sebastes_jordani:9.408429):1.21622,((Sebastes_aurora:3.496853,Sebastes_diploproa:3.496853):1.244081,(Sebastes_ruberrimus:4.274649,Sebastes_fasciatus:4.274649):0.466285):5.883715):5.129756):19.156136):8.779324,((Setarches_guentheri:33.436106,(Neomerinthe_hemingwayi:20.484462,(Pontinus_rathbuni:3.853914,Pontinus_longispinis:3.853914):16.630548):12.951644):6.678922,((Iracundus_signifer:23.086785,(Sebastapistes_cyanostigma:20.617551,(Caracanthus_maculatus:2.159477,Caracanthus_unipinna:2.159477):18.458074):2.469234):2.088979,((Taenianotus_triacanthus:18.953571,(Scorpaenopsis_longispina:8.125232,Scorpaenopsis_oxycephala:8.125232):10.828339):3.739619,((Scorpaena_brasiliensis:13.646687,Scorpaena_agassizii:13.646687):3.342477,(Scorpaena_guttata:7.421967,Scorpaena_dispar:7.421967):9.567197):5.704026):2.482574):14.939264):3.574837):2.567776):16.25346):3.97518):2.869033):3.752256,((Platycephalus_indicus:46.800937,(Rogadius_asper:27.226186,(Sunagocia_arenicola:5.504031,Thysanophrys_chiltonae:5.504031):21.722155):19.574751):23.994488,((Hoplichthys_langsdorfii:3.414302,Hoplichthys_gilberti:3.414302):62.659134,(Anoplopoma_fimbria:46.504651,((Rathbunella_hypoplecta:22.798585,((Bathymaster_caeruleofasciatus:5.087961,Bathymaster_signatus:5.087961):13.471246,(Cebidichthys_violaceus:15.585444,(Bryozoichthys_marjorius:14.216617,((Zoarces_americanus_viviparus:8.258259,(Lycenchelys_crotalinus:6.498597,(Bothrocara_hollandi:6.271915,(Lycodes_diapterus:5.824329,(Eucryphycus_californicus:5.439429,((Lycodapus_mandibularis:2.916574,Bothrocara_brunneum:2.916574):2.096831,(Melanostigma_pammelas:4.14763,(Lycodes_terraenovae:3.192163,Lycodes_brevipes:3.192163):0.955467):0.865775):0.426024):0.3849):0.447586):0.226682):1.759662):4.235336,((Anarrhichthys_ocellatus:3.233746,(Anarhichas_orientalis_lupus:1.992454,Anarhichas_denticulatus:1.992454):1.241292):4.696696,(Zaprora_silenus:7.397642,((Pholis_ornata:2.250673,Pholis_crassispina:2.250673):4.632989,(Cryptacanthodes_maculatus:6.26139,(Poroclinus_rothrocki:5.349006,(Leptoclinus_maculatus:3.948126,(Lumpenus_lampretaeformis:3.933508,Lumpenus_fabricii:3.933508):0.014618):1.40088):0.912384):0.622272):0.51398):0.5328):4.563153):1.723022):1.368827):2.973763):4.239378):19.028762,(((Aulorhynchus_flavidus:25.280384,(Hypoptychus_dybowskii:22.287004,Aulichthys_japonicus:22.287004):2.99338):1.019617,((Culaea_inconstans:19.844902,(Apeltes_quadracus:17.136647,Spinachia_spinachia:17.136647):2.708255):1.782128,(Pungitius_pungitius:16.827668,(Gasterosteus_aculeatus:8.991218,Gasterosteus_wheatlandi:8.991218):7.83645):4.799362):4.672971):13.534822,(Zaniolepis_frenata:33.581561,((Pleurogrammus_monopterygius:9.941558,(Hexagrammos_lagocephalus_otakii:4.4984,Hexagrammos_decagrammus:4.4984):5.443158):17.877416,((Trichodon_trichodon:22.810058,((Eumicrotremus_orbis:9.248856,Cyclopterus_lumpus:9.248856):11.51354,((Liparis_pulchellus:8.310921,Liparis_gibbus:8.310921):3.161614,((Careproctus_rastrinus:5.256799,Careproctus_melanurus:5.256799):4.213251,(Rhinoliparis_barbulifer:7.043116,(Paraliparis_copei:6.145461,(Paraliparis_hystrix:4.676096,Paraliparis_beani:4.676096):1.469365):0.897655):2.426934):2.002485):9.289861):2.047662):1.989944,(((Artediellus_uncinatus:16.740687,Scorpaenichthys_marmoratus:16.740687):2.351409,((Hypsagonus_quadricornis:14.409019,(Hemilepidotus_jordani:3.585276,Hemilepidotus_zapus:3.585276):10.823743):0.867894,((Sarritor_frenatus:4.982991,Sarritor_leptorhynchus:4.982991):5.478246,(Aspidophoroides_monopterygius:8.936652,(Stellerina_xyosterna:7.668274,(Bathyagonus_alascanus:5.475611,(Xeneretmus_latifrons:3.25175,Bathyagonus_pentacanthus:3.25175):2.223861):2.192663):1.268378):1.524585):4.815676):3.815183):1.279292,(Cottus_carolinae:18.193597,((Rastrinus_scutiger:12.737968,(Chitonotus_pugetensis:11.273779,(Icelinus_filamentosus:3.107033,Icelinus_quadriseriatus:3.107033):8.166746):1.464189):2.594817,((Gymnocanthus_galeatus:12.232601,Leptocottus_armatus:12.232601):2.628202,((Enophrys_taurina:11.853523,(Radulinus_asprellus:8.138826,(Myoxocephalus_octodecemspinosus:4.585021,(Microcottus_sellaris:3.25996,Myoxocephalus_polyacanthocephalus:3.25996):1.325061):3.553805):3.714697):2.17108,((Triglops_macellus:7.56846,Triglops_scepticus:7.56846):5.40511,(Dasycottus_setiger:10.723493,(Malacocottus_zonurus:10.180273,(Cottunculus_thomsonii:9.174171,Psychrolutes_phrictus:9.174171):1.006102):0.54322):2.250077):1.051033):0.8362):0.471982):2.860812):2.177791):4.428614):3.018972):5.762587):6.253262):1.992524):4.677304):19.568785):4.721989):2.312145):2.850582):2.619154):3.622695)Perciformes:12.7):0.370939):0.522413):0.506648):8.5)Eupercaria:7.0993):4.591565):5.109134):5.2):6.0)Percomorphaceae:12.2):1.463665)Euacanthomorphacea:8.336335):6.583092)Acanthomorphata:11.716908)Ctenosquamata:9.7):9.5)Neoteleostei:19.0):3.554892):16.945108)Euteleosteomorpha:18.8)Clupeocephala:23.2)Osteoglossocephalai:9.5)Teleostei:39.2)Neopterygii:27.6)Actinopteri:32.5)Actinopterygii:42.2)Osteichthyes:37.6,CHONDRICHTHYES@:462.4); 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Trichomycterus_sp:105.886773,((Loricaria_simillima:70.314063,Astroblepus_sp:70.314063):28.122065,(Callichthys_callichthys:69.2,(Corydoras_trilineatus:40.456696,Corydoras_aurofrenatus:40.456696):28.743304):29.236128):7.450645):4.762206):5.151021,(Diplomystes_nahuelbutaensis:106.204156,((Clarias_batrachus:47.601763,Heteropneustes_fossilis:47.601763):38.718355,(((Bagarius_yarrelli:55.522683,(Liobagrus_aequilabris:48.028166,Akysis_sp:48.028166):7.494517):21.359019,((Horabagrus_brachysoma:59.629878,Pseudeutropius_brachypopterus:59.629878):14.819689,(Mystus_bocourti:36.078433,Bagrus_ubangensis:36.078433):38.371134):2.432135):8.407973,(((Chaca_sp:72.429965,(Helogenes_marmoratus:57.16588,Cetopsis_coecutiens:57.16588):15.264085):10.714848,(Cranoglanis_bouderius:68.699999,(Ictalurus_punctatus:39.099999,Ameiurus_natalis:39.099999):29.6):14.444814):1.039632,((Pangasianodon_hypophthalmus:80.594984,(Gogo_arcuatus:69.1,Ariopsis_felis_seemanni:69.1):11.494984):1.563582,(((Chrysichthys_sp:6.269994,Chrysichthys_dendrophorus:6.269994):67.584437,(Amphilius_jacksonii:69.200236,(Malapterurus_beninensis:64.740777,Synodontis_batesii:64.740777):4.459459):4.654195):6.339371,((Plotosus_lineatus:73.040117,Hemisilurus_moolenburghi:73.040117):5.503896,((Ageneiosus_atronasus:51.102018,Anduzedoras_oxyrhynchus:51.102018):23.797937,(Goeldiella_eques:57.155894,(Pseudopimelodus_mangurus:46.825924,Brachyplatystoma_filamentosum:46.825924):10.32997):17.744061):3.644058):1.649789):1.964764):2.025879):1.10523):1.030443):19.884038):9.595844)Siluriformes:21.212154)Characiphysae:10.822489):25.065357)Otophysi:25.7)Ostariophysi:21.098547):10.501453)Otomorpha:20.4,(Lepidogalaxias_salamandroides:231.8,(((Bathylagus_euryops:70.712354,(Nansenia_longicauda_ardesiaca:51.558629,(Macropinna_microstoma:33.234078,(Argentina_sialis_silus:13.624567,Argentina_striata:13.624567):19.609511):18.324551):19.153725)Argentiniformes:88.887646,((Aplochiton_taeniatus:50.0,(Galaxiella_nigrostriata:42.605636,(Neochanna_burrowsius:34.522004,(Brachygalaxias_bullocki:32.495985,Galaxias_maculatus:32.495985):2.026019):8.083632):7.394364)Galaxiiformes:95.636629,(((Esox_lucius:31.386513,Esox_americanus:31.386513):48.013487,(Umbra_limi:55.772876,Novumbra_hubbsi:55.772876):23.627124)Esociformes:25.078403,(Coregonus_clupeaformis:35.3,(Thymallus_brevirostris:32.464307,(Oncorhynchus_nerka_mykiss:19.947525,(Salvelinus_alpinus:16.756184,(Salmo_salar:14.861468,Parahucho_perryi:14.861468):1.894716):3.191341):12.516782):2.835693)Salmoniformes:69.178403):41.158226):13.963371)Protacanthopterygii:55.254892,((((Retropinna_semoni:22.529514,Stokellia_anisodon:22.529514):51.170486,(((Osmerus_mordax:10.347393,Thaleichthys_pacificus:10.347393):5.877349,(Mallotus_villosus:14.980242,Hypomesus_pretiosus:14.980242):1.2445):18.137763,(Plecoglossus_altivelis:28.725469,((Neosalanx_jordani:10.487235,Neosalangichthys_ishikawae:10.487235):2.238638,(Salanx_cuvieri:7.987388,Leucosoma_reevesii:7.987388):4.738485):15.999596):5.637036):39.337495)Osmeriformes:55.7,((Diplophos_taenia:77.34295,((Bonapartia_pedaliota:54.320038,Margrethia_obtusirostra:54.320038):20.007411,(Gonostoma_elongatum:69.964426,Cyclothone_microdon:69.964426):4.363023):3.015501):6.45705,(Pollichthys_mauli:77.73342,((Polymetme_corythaeola_sp:67.565698,(Polyipnus_spinifer:60.02376,((Argyropelecus_gigas:10.75016,Argyropelecus_affinis:10.75016):14.493519,(Sternoptyx_sp:20.932156,Maurolicus_weitzmani:20.932156):4.311523):34.780081):7.541938):5.012869,((Chauliodus_sloani:20.419989,Chauliodus_macouni_danae:20.419989):42.727184,((Borostomias_antarcticus:23.038554,Neonesthes_capensis:23.038554):17.725111,((Heterophotus_ophistoma:34.302727,(Stomias_boa:27.141257,Rhadinesthes_decimus:27.141257):7.16147):1.805224,(Astronesthes_leucopogon:35.402261,(Chirostomias_pliopterus:31.596407,((Melanostomias_margaritifer:21.804032,Leptostomias_longibarba:21.804032):5.231986,((Photonectes_margarita:19.065425,Tactostoma_macropus:19.065425):7.217791,(Photostomias_guernei:24.056719,(Malacosteus_niger:23.385989,(Eustomias_polyaster:23.058022,(Aristostomias_scintillans:23.044458,Bathophilus_flemingi_pawneei:23.044458):0.013564):0.327967):0.67073):2.226497):0.752802):4.560389):3.805854):0.70569):4.655714):22.383508):9.431394):5.154853):6.06658)Stomiatiformes:45.6)Stomiatii:81.9,((Ateleopus_japonicus:8.100975,(Ijimaia_antillarum:1.851199,Ijimaia_loppei:1.851199):6.249776)Ateleopodiformes:184.199025,(((Synodus_variegatus:50.706529,(Trachinocephalus_myops:34.936529,Synodus_foetens:34.936529):15.77):63.193471,(((Pseudotrichonotus_altivelis:85.069082,Paraulopus_oblongus:85.069082):16.922086,(Saurida_gracilis:50.265907,(Harpadon_microchir:42.546554,Saurida_undosquamis:42.546554):7.719353):51.725261):8.324299,(((Aulopus_filamentosus:47.181996,Bathysaurus_ferox:47.181996):10.847641,(Bathypterois_grallator:52.456704,Ipnops_sp:52.456704):5.572933):23.632996,((Bathypterois_atricolor:69.35022,(Gigantura_indica:13.530161,Gigantura_chuni:13.530161):55.820059):6.463444,((Benthalbella_macropinna:31.410754,(Benthalbella_dentata:8.014963,Benthalbella_infans:8.014963):23.395791):31.100655,((Chlorophthalmus_agassizi:56.023798,Scopelarchus_sp:56.023798):5.132849,(Parasudis_truculenta:59.829934,((Ahliesaurus_berryi:25.638925,Scopelosaurus_lepidus:25.638925):33.459363,(Sudis_atrox:55.043996,((Anotopterus_pharao:45.676404,(Omosudis_lowii:36.295606,(Alepisaurus_brevirostris:28.879812,Alepisaurus_ferox:28.879812):7.415794):9.380798):8.24094,((Stemonosudis_intermedia_macrura:38.680633,Lestidiops_jayakari:38.680633):11.457751,((Evermannella_balbo:17.517053,Coccorella_atlantica:17.517053):29.184168,(Paralepis_coregonoides:36.168036,(Notolepis_coatsi:0.46445,Magnisudis_prionosa:0.46445):35.703586):10.533185):3.437163):3.77896):1.126652):4.054292):0.731646):1.326713):1.354762):13.302255):5.848969):28.652834):3.584533)Aulopiformes:68.9,((((Neoscopelus_macrolepidotus:21.513581,Neoscopelus_microchir:21.513581):20.906388,(Scopelengys_sp:5.004968,Scopelengys_tristis:5.004968):37.415001):31.180031,(((Notolychnus_valdiviae:40.191883,Lobianchia_gemellarii:40.191883):5.72165,(Lampadena_speculigera:39.826216,((Lepidophanes_guentheri:21.437275,(Ceratoscopelus_maderensis:10.546561,Ceratoscopelus_warmingii:10.546561):10.890714):16.309947,(Stenobrachius_leucopsarus:31.265086,(Nannobrachium_lineatum:26.763615,(Lampanyctus_macdonaldi:25.484025,Lampanyctus_jordani:25.484025):1.27959):4.501471):6.482136):2.078994):6.087317):5.783799,((Notoscopelus_caudispinosus_resplendens:34.855362,(Gymnoscopelus_nicholsi:16.628589,(Gymnoscopelus_opisthopterus:4.496984,Gymnoscopelus_braueri:4.496984):12.131605):18.226773):10.019237,((Diaphus_sp:15.207586,(Symbolophorus_californiensis:10.112905,Diaphus_rafinesquii:10.112905):5.094681):25.47779,((Electrona_antarctica:14.428311,(Protomyctophum_choriodon:3.104448,Krefftichthys_anderssoni:3.104448):11.323863):15.182154,(Benthosema_glaciale:28.308863,(Myctophum_punctatum:26.445526,((Tarletonbeania_crenularis:21.421451,Symbolophorus_evermanni:21.421451):2.82265,(Hygophum_hygomii:16.998146,Hygophum_proximum:16.998146):7.245955):2.201425):1.863337):1.301602):11.074911):4.189223):6.822733):21.902668)Myctophiformes:99.5,(((Lophotus_lacepede:81.7,(Lampris_guttatus:65.554566,((Regalecus_russelii:12.163691,Regalecus_glesne:12.163691):25.521954,(Desmodema_polystictum:29.911651,(Zu_cristatus:24.186495,(Trachipterus_trachypterus:0.7242,Trachipterus_arcticus:0.7242):23.462295):5.725156):7.773994):27.868921):16.145434)Lampridiformes:68.6,(((Percopsis_transmontana:14.617956,Percopsis_omiscomaycus:14.617956):48.582044,(Aphredoderus_sayanus:41.5,(Speoplatyrhinus_poulsoni:10.886201,(Chologaster_cornuta:10.2227,Troglichthys_rosae:10.2227):0.663501):30.613799):21.7)Percopsiformes:71.791036,((Cyttomimus_affinis:66.46081,(Cyttopsis_rosea:49.2,(Zenopsis_conchifer:33.5,Zeus_faber:33.5):15.7):17.26081)Zeiformes:40.63919,(Stylephorus_chordatus:78.8,((Merluccius_bilinearis:4.814876,Merluccius_productus:4.814876):40.84028,(((Gadomus_dispar:9.947709,Bathygadus_favosus:9.947709):28.939232,(Steindachneria_argentea:35.929201,((Malacocephalus_laevis:17.761913,(Trachonurus_sulcatus:15.56595,(Nezumia_liolepis:6.541893,(Nezumia_bairdii:2.978829,Nezumia_aequalis:2.978829):3.563064):9.024057):2.195963):10.126442,(Macrourus_sp:21.899459,((Coelorinchus_caribbaeus:9.832863,Coelorinchus_caelorhincus:9.832863):12.050918,((Coryphaenoides_armatus:8.705829,Coryphaenoides_rupestris:8.705829):4.710541,(Coryphaenoides_cinereus:4.721775,(Coryphaenoides_acrolepis:1.374281,Albatrossia_pectoralis:1.374281):3.347494):8.694595):8.467411):0.015678):5.988896):8.040846):2.95774):2.613059,((Muraenolepis_marmorata:36.494611,(Physiculus_fulvus:29.55261,((Laemonema_goodebeanorum:2.50946,Laemonema_barbatulum:2.50946):22.579308,(Halargyreus_johnsonii:16.444964,(Lepidion_ensiferus:5.357055,(Antimora_rostrata:0.544543,Antimora_microlepis:0.544543):4.812512):11.087909):8.643804):4.463842):6.942001):1.765507,((Phycis_chesteri:8.038659,(Urophycis_tenuis:5.240437,(Urophycis_regia:4.089467,Urophycis_chuss:4.089467):1.15097):2.798222):25.809917,((Enchelyopus_cimbrius:12.351856,(Gaidropsarus_ensis:1.063842,Gaidropsarus_argentatus:1.063842):11.288014):17.448721,(Lota_lota:23.935378,(Micromesistius_poutassou:16.109498,((Gadus_chalcogrammus:10.882127,Microgadus_proximus:10.882127):0.783593,(Pollachius_virens:7.113828,((Melanogrammus_aeglefinus:4.86848,Merlangius_merlangus:4.86848):0.835458,(Gadus_morhua:3.387041,Gadus_ogac:3.387041):2.316897):1.40989):4.551892):4.443778):7.82588):5.865199):4.047999):4.411542):3.239882):4.155156)Gadiformes:33.144844)Gadariae:28.3)Zeiogadaria:27.891036)Paracanthomorphacea:15.308964):11.083092,((Polymixia_japonica:13.716067,Polymixia_lowei:13.716067)Polymixiiformes:141.083933,((((Diretmus_argenteus:19.059513,Diretmichthys_parini:19.059513):34.941385,((Monocentris_japonica:27.989531,Anomalops_katoptron:27.989531):5.610469,((Hoplostethus_occidentalis_atlanticus:24.361642,Gephyroberyx_darwinii:24.361642):7.918771,(Anoplogaster_cornuta:31.227875,(Paratrachichthys_sajademalensis:17.556284,Aulotrachichthys_prosthemius:17.556284):13.671591):1.052538):1.319587):20.400898):71.278167,(((Beryx_decadactylus:27.236685,Centroberyx_druzhinini:27.236685):43.380061,((Poromitra_crassiceps:24.92187,Scopeloberyx_sp:24.92187):14.219431,(Scopelogadus_beanii:32.606123,(Melamphaes_suborbitalis:16.3971,Melamphaes_lugubris_polylepis:16.3971):16.209023):6.535178):31.475445):40.297009,(((Rondeletia_bicolor:18.618697,Rondeletia_loricata:18.618697):36.665959,(Barbourisia_rufa:46.226385,Acanthochaenus_luetkenii:46.226385):9.058271):34.605995,(Cetostoma_regani:55.49634,(Gyrinomimus_bruuni:21.253796,(Cetomimus_craneae:10.538682,(Gyrinomimus_parri_sp:6.885037,Cetomimus_sp:6.885037):3.653645):10.715114):34.242544):34.394311):21.023104):14.36531)Beryciformes:21.1846,((((Ostichthys_trachypoma:25.197942,(Plectrypops_lima:11.854458,Plectrypops_retrospinis:11.854458):13.343484):5.908719,((Myripristis_murdjan:6.23309,Myripristis_violacea:6.23309):7.08274,(Myripristis_vittata:7.901223,(Myripristis_hexagona:5.776899,Myripristis_berndti:5.776899):2.124324):5.414607):17.790831):21.393339,((Sargocentron_diadema:25.435851,(Holocentrus_rufus:20.788943,(Sargocentron_caudimaculatum:7.933452,Sargocentron_tiere:7.933452):12.855491):4.646908):3.038179,(Sargocentron_cornutum:24.250917,(Neoniphon_marianus:21.359673,(Sargocentron_coruscum:18.908724,(Sargocentron_vexillarium:15.375325,(Neoniphon_argenteus:9.482813,(Neoniphon_opercularis:7.311804,Neoniphon_sammara:7.311804):2.171009):5.892512):3.533399):2.450949):2.891244):4.223113):24.02597)Holocentriformes:92.5,((((Diancistrus_sp:6.205133,Dinematichthys_iluocoeteoides:6.205133):35.622423,(Brosmophycis_marginata:28.531275,((Bidenichthys_capensis:20.411323,(Cataetyx_rubrirostris_lepidogenys:19.611923,Barathronus_maculatus:19.611923):0.7994):2.21586,(Brosmophyciops_pautzkei:16.329087,(Diplacanthopoma_brunnea:8.885971,Diplacanthopoma_brachysoma:8.885971):7.443116):6.298096):5.904092):13.296281):33.572444,((Brotula_barbata:17.13037,Brotula_multibarbata:17.13037):49.097347,(Petrotyx_sanguineus:56.148577,((Bassogigas_gillii:46.424594,(Carapus_bermudensis:36.660247,(Pyramodon_ventralis:4.466651,Onuxodon_parvibrachium:4.466651):32.193596):9.764347):3.154399,((Lamprogrammus_niger:29.409604,(Brotulotaenia_crassa:2.054745,Brotulotaenia_nigra:2.054745):27.354859):15.269313,(Dicrolene_introniger:43.465872,(Neobythites_gilli:38.843863,((Lepophidium_profundorum:11.854747,(Lepophidium_brevibarbe:9.439783,Lepophidium_jeannae:9.439783):2.414964):11.181996,(Genypterus_blacodes:21.59118,(Chilara_taylori:9.435137,(Ophidion_holbrookii:7.404977,(Ophidion_robinsi:3.816636,Ophidion_josephi:3.816636):3.588341):2.03016):12.156043):1.445563):15.80712):4.622009):1.213045):4.900076):6.569584):10.07914):9.172283)Ophidiiaria:57.4,(((Porichthys_notatus:16.879114,Porichthys_plectrodon:16.879114):22.920886,(Batrachoides_pacifici:27.049326,(Sanopus_sp:23.92031,(Opsanus_tau:16.982491,(Opsanus_pardus:4.281706,Opsanus_beta:4.281706):12.700785):6.937819):3.129016):12.750674)Batrachoidaria:87.0,((((Kurtus_indicus:28.882532,Kurtus_gulliveri:28.882532):51.417468,(Pseudamia_gelatinosa:66.307221,(Gymnapogon_urospilotus:39.694196,(Fowleria_aurita:34.463005,((Apogon_campbelli:26.4696,(Cercamia_eremia:23.908259,(Phaeoptyx_pigmentaria:11.611893,(Astrapogon_puncticulatus:0.023741,Astrapogon_stellatus:0.023741):11.588152):12.296366):2.561341):2.957716,(Rhabdamia_cypselura:28.04049,((Nectamia_bandanensis:11.67233,Nectamia_fusca:11.67233):13.919677,((Pristiapogon_exostigma:17.0033,Sphaeramia_orbicularis:17.0033):3.673746,((Ostorhinchus_cookii:15.106505,Cheilodipterus_isostigmus:15.106505):1.061854,((Pterapogon_kauderni:14.744372,Archamia_biguttata:14.744372):0.718897,(Ostorhinchus_lateralis:13.931253,Cheilodipterus_quinquelineatus:13.931253):1.532016):0.70509):4.508687):4.914961):2.448483):1.386826):5.035689):5.231191):26.613025):13.992779)Kurtiformes:22.0,((Odontobutis_potamophila:18.184092,Perccottus_glenii:18.184092):54.615908,(((Oxyeleotris_selheimi:21.63371,Ophiocara_porocephala:21.63371):32.446537,(Dormitator_maculatus:35.276288,Eleotris_acanthopoma_pisonis:35.276288):18.803959):10.350561,(((Gnatholepis_anjerensis:38.174501,Periophthalmus_kalolo:38.174501):5.889022,(Lepidogobius_lepidus:35.790997,(Ctenogobius_boleosoma:21.284121,(Gnatholepis_cauerensis:19.128476,Evorthodus_lyricus:19.128476):2.155645):14.506876):8.272526):10.736043,((Bathygobius_mystacium:40.060582,(Psammogobius_biocellatus:33.064552,(Stonogobiops_nematodes:29.430355,Amblygobius_decussatus:29.430355):3.634197):6.99603):7.789401,((Bollmannia_communis:41.827351,(Gobiosoma_bosc:24.842103,(Elacatinus_oceanops:15.835871,Risor_ruber:15.835871):9.006232):16.985248):3.803827,((Amblygobius_phalaena:33.852188,(Valenciennea_strigata:22.658599,Valenciennea_puellaris:22.658599):11.193589):8.455677,((((Priolepis_cincta:12.807478,Priolepis_hipoliti:12.807478):19.559227,(Lythrypnus_dalli:24.235618,(Trimma_caesiura:11.648806,(Trimma_haima:8.86234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311127):21.920866,((((((Monopterus_albus:69.152565,(Indostomus_paradoxus:2.692657,Indostomus_crocodilus:2.692657):66.459908):4.547573,(Macrognathus_siamensis:18.064552,(Mastacembelus_erythrotaenia:7.602283,(Mastacembelus_niger:7.070436,(Mastacembelus_brachyrhinus:2.807681,Mastacembelus_cunningtoni:2.807681):4.262755):0.531847):10.462269):55.635586)Synbranchiformes:6.999862,(((Ctenopoma_kingsleyae:33.074312,Microctenopoma_nanum:33.074312):29.724657,((Trichopodus_pectoralis:45.626493,Betta_splendens:45.626493):14.077746,Helostoma_temminkii:59.704239):3.09473):7.867293,((Channa_lucius:35.481445,(Channa_striata:16.235812,Channa_melasoma:16.235812):19.245633):31.96482,((Pristolepis_sp:14.79164,Pristolepis_fasciata:14.79164):48.798177,((Dario_dario:38.556398,Badis_pyema:38.556398):6.970876,(Nandus_nebulosus:12.970614,(Nandus_andrewi:1.360622,Nandus_nandus:1.360622):11.609992):32.55666):18.062543):3.856448):3.219997)Anabantiformes:10.033738)Anabantaria:15.7,((Nematistius_pectoralis:60.09561,((Coryphaena_hippurus:19.129261,Rachycentron_canadum:19.129261):12.770739,(Remora_osteochir_australis:10.181739,(Phtheirichthys_lineatus:1.848715,(Echeneis_naucrates:0.500665,Echeneis_neucratoides:0.500665):1.34805):8.333024):21.718261):28.19561):9.30439,((((Sphyraena_putnamae:18.204293,(Sphyraena_jello:10.332121,Sphyraena_barracuda:10.332121):7.872172):20.141759,(Sphyraena_japonica:20.644035,(Sphyraena_sphyraena:13.957629,Sphyraena_argentea:13.957629):6.686406):17.702017):27.571991,(Mene_maculata:60.366767,(Leptomelanosoma_indicum:17.701093,((Polydactylus_octonemus:1.175876,Polydactylus_virginicus:1.175876):15.036527,(Polydactylus_sextarius:14.030604,(Eleutheronema_rhadinum:4.364669,Eleutheronema_tetradactylum:4.364669):9.665935):2.181799):1.48869):42.665674):5.551276):2.881957,((((Leptobrama_muelleri:46.74854,(Toxotes_jaculatrix:5.197436,Toxotes_chatareus:5.197436):41.551104):5.100583,(Xiphias_gladius:27.944272,(Kajikia_albida:5.679945,((Makaira_sp:0.432391,Makaira_nigricans:0.432391):4.487487,(Istiophorus_platypterus:4.068899,Tetrapturus_angustirostris:4.068899):0.850979):0.760067):22.264327)Istiophoriformes:23.904851):5.268959,(((Scomberoides_lysan:21.219545,Oligoplites_saurus:21.219545):17.792734,(Trachinotus_ovatus:13.314295,(Trachinotus_carolinus:9.406599,Trachinotus_falcatus:9.406599):3.907696):25.697984):13.258708,((Elagatis_bipinnulata:37.121685,(Seriola_rivoliana:2.736423,Seriola_dumerili:2.736423):34.385262):12.878315,((Selar_crumenophthalmus:19.039156,(Trachurus_lathami:14.233199,(Decapterus_macarellus:9.835702,Decapterus_punctatus:9.835702):4.397497):4.805957):10.815977,(((Uraspis_secunda:12.59363,Carangoides_ferdau:12.59363):4.431692,(Carangoides_plagiotaenia:14.464621,(Alectis_ciliaris:12.400521,(Selene_setapinnis:4.199124,Selene_brownii:4.199124):8.201397):2.0641):2.560701):8.762253,((Atule_mate:19.595354,Gnathanodon_speciosus:19.595354):2.99285,((Chloroscombrus_chrysurus:16.12094,Hemicaranx_amblyrhynchus:16.12094):4.09982,(Caranx_crysos_ruber:11.659237,(Caranx_ignobilis:5.894184,Caranx_sexfasciatus:5.894184):5.765053):8.561523):2.367444):3.199371):4.067558):20.144867):2.270987):4.847095):4.483123,((Psettodes_erumei:11.554984,Psettodes_belcheri:11.554984):47.878181,(((Centropomus_undecimalis:18.591092,(Centropomus_viridis:11.439461,(Centropomus_ensiferus:9.747409,Centropomus_medius:9.747409):1.692052):7.151631):33.308908,(Psammoperca_waigiensis:32.050648,(Lates_calcarifer:12.768362,(Lates_japonicus:9.697422,Lates_microlepis:9.697422):3.07094):19.282286):19.849352):6.052595,((Lepidoblepharon_ophthalmolepis:41.293483,(Citharoides_macrolepis:16.362693,Citharus_linguatula:16.362693):24.93079):12.306517,(((Trinectes_maculatus:21.130154,((Hypoclinemus_sp:13.017378,Achirus_lineatus:13.017378):4.716285,(Gymnachirus_texae:0.95788,Gymnachirus_melas:0.95788):16.775783):3.396491):29.434162,((Plagiopsetta_glossa:10.222577,(Samariscus_xenicus:5.445401,(Samariscus_latus:1.431842,Samariscus_japonicus:1.431842):4.013559):4.777176):38.678555,((Poecilopsetta_plinthus:1.380407,Poecilopsetta_beanii:1.380407):44.414968,((Cynoglossus_interruptus:37.589307,(Symphurus_atricaudus:14.112178,(Symphurus_civitatium:4.483656,Symphurus_plagiusa:4.483656):9.628522):23.477129):4.810693,((Aseraggodes_heemstrai:16.814795,Aseraggodes_kobensis:16.814795):15.728788,((Microchirus_frechkopi:13.571956,(Solea_solea:8.376781,Pegusa_lascaris:8.376781):5.195175):11.420474,(Heteromycteris_japonicus:21.514274,(Brachirus_annularis:9.83189,(Pseudaesopia_japonica:4.329537,Soleichthys_heterorhinos:4.329537):5.502353):11.682384):3.478156):7.551153):9.856417):3.395375):3.105757):1.663184):1.527715,(((Scophthalmus_maximus:28.781036,(Scophthalmus_aquosus:23.377292,Lepidorhombus_boscii:23.377292):5.403744):17.657396,(Oncopterus_darwinii:33.462802,((Mancopsetta_maculata:0.642821,Neoachiropsetta_milfordi:0.642821):21.848025,(Rhombosolea_leporina:4.689959,(Rhombosolea_tapirina:1.43641,Rhombosolea_plebeia:1.43641):3.253549):17.800887):10.971956):12.97563):3.872127,(((Paralichthys_dentatus:34.43969,((Cyclopsetta_chittendeni:12.257242,Syacium_micrurum:12.257242):18.779966,(Citharichthys_sordidus:17.474326,(Citharichthys_arctifrons:14.706003,(Etropus_crossotus:11.508059,Etropus_microstomus:11.508059):3.197944):2.768323):13.562882):3.402482):6.355634,(Laeops_kitaharae:18.800001,(Chascanopsetta_lugubris:17.9796,((Bothus_lunatus:13.322564,Bothus_robinsi:13.322564):4.413016,((Monolene_sp:14.104021,Trichopsetta_ventralis:14.104021):2.837074,(Asterorhombus_cocosensis:15.876155,(Psettina_tosana:12.742948,(Arnoglossus_blachei:6.90431,Arnoglossus_imperialis:6.90431):5.838638):3.133207):1.06494):0.794485):0.24402):0.820401):21.995323):4.386767,((Xystreurys_liolepis:17.395832,(Pseudorhombus_pentophthalmus:16.378967,((Gastropsetta_frontalis:3.26495,Ancylopsetta_ommata:3.26495):8.785002,(Paralichthys_californicus:6.786751,Paralichthys_albigutta:6.786751):5.263201):4.329015):1.016865):4.08644,(Atheresthes_evermanni:19.686963,(Hypsopsetta_guttulata:17.244973,(((Glyptocephalus_zachirus:5.117694,(Embassichthys_bathybius:3.72555,Microstomus_pacificus:3.72555):1.392144):2.549352,(Lyopsetta_exilis:5.963901,(Hippoglossus_hippoglossus:5.106949,Eopsetta_jordani:5.106949):0.856952):1.703145):2.223697,((Limanda_limanda:4.588583,Hippoglossoides_elassodon:4.588583):3.218528,(Pseudopleuronectes_americanus:6.96439,((Platichthys_stellatus:3.732552,Pleuronectes_platessa:3.732552):2.370544,(Parophrys_vetulus:4.449471,(Lepidopsetta_bilineata:4.099454,(Isopsetta_isolepis:3.813873,Psettichthys_melanostictus:3.813873):0.285581):0.350017):1.653625):0.861294):0.842721):2.083632):7.35423):2.44199):1.795309):23.699819):5.128468):1.781472):1.507969):4.352595):1.48057):2.16804):7.198795):0.6)Carangiaria:27.0):12.050153,((((Polycentropsis_abbreviata:46.103084,(Monocirrhus_polyacanthus:27.472033,Polycentrus_schomburgkii:27.472033):18.631051):48.114875,(Pholidichthys_leucotaenia:88.7,((Etroplus_maculatus:49.297945,Paretroplus_maculatus:49.297945):27.102055,((Paratilapia_polleni:48.325588,Ptychochromis_grandidieri:48.325588):20.810997,((Cichla_temensis:52.934446,(Crenicichla_lepidota:50.100001,(Herichthys_cyanoguttatus:23.172861,(Symphysodon_discus:17.001924,Heros_efasciatus:17.001924):6.170937):26.92714):2.834445):8.965484,(Heterochromis_multidens:57.250288,(Nanochromis_parilus:29.79536,(Oreochromis_niloticus:18.346974,(Tilapia_louka:15.389183,(Steatocranus_gibbiceps:12.134063,(Neolamprologus_brichardi:9.183198,(Astatotilapia_burtoni:4.073468,(Pundamilia_nyererei:2.748366,Maylandia_zebra:2.748366):1.325102):5.10973):2.950865):3.25512):2.957791):11.448386):27.454928):4.649642):7.236655):7.263415)Cichliformes:12.3)Cichlomorphae:5.517959):0.428115,((((Atherinopsis_californiensis:20.110119,((Odontesthes_argentinensis:3.243131,Odontesthes_humensis:3.243131):4.430301,(Odontesthes_retropinnis:1.282477,Odontesthes_bonariensis:1.282477):6.390955):12.436687):28.607397,(Membras_martinica:26.507117,(Labidesthes_sicculus:14.034561,((Poblana_ferdebueni:5.445417,Menidia_beryllina:5.445417):1.240313,(Menidia_menidia:5.800579,Menidia_peninsulae:5.800579):0.885151):7.348831):12.472556):22.210399):22.224664,(Iso_sp:49.320038,(Rheocles_wrightae:45.587422,((Craterocephalus_honoriae:40.343535,(Atherinomorus_stipes:27.417921,(Atherinomorus_lacunosus:18.10875,Atherinomorus_vaigiensis:18.10875):9.309171):12.925614):3.445895,((Rhadinocentrus_ornatus:23.847475,(Melanotaenia_splendida:10.116474,(Melanotaenia_sp:6.026677,Melanotaenia_trifasciata:6.026677):4.089797):13.731001):16.025407,(Marosatherina_ladigesi:33.738999,(Phenacostethus_smithi:27.920636,(Pseudomugil_gertrudae:17.876274,Pseudomugil_signifer:17.876274):10.044362):5.818363):6.133883):3.916548):1.797992):3.732616):21.622142)Atheriniformes:6.45782,((Pachypanchax_playfairii:66.88735,((Poecilia_latipinna_reticulata:14.292785,(Poeciliopsis_elongata:12.312835,(Heterandria_formosa:11.367362,(Gambusia_affinis:5.73674,Belonesox_belizanus:5.73674):5.630622):0.945473):1.97995):30.131968,((Floridichthys_carpio:20.456976,(Cyprinodon_variegatus:13.822603,Jordanella_floridae:13.822603):6.634373):20.014113,(Fundulus_parvipinnis:18.797065,((Fundulus_heteroclitus:12.933656,Lucania_parva_goodei:12.933656):1.1775,(Adinia_xenica:11.46608,(Fundulus_blairae:10.804496,Fundulus_chrysotus:10.804496):0.661584):2.645076):4.685909):21.674024):3.953664):22.462597)Cyprinodontiformes:9.514255,(Oryzias_latipes:71.879041,((Zenarchopterus_dispar:32.763495,(Dermogenys_collettei:29.885486,((Xenentodon_cancila:17.254219,(Tylosurus_crocodilus:6.568468,Ablennes_hians:6.568468):10.685751):6.744727,(Strongylura_notata:20.277008,(Platybelone_argalus:18.768659,(Cololabis_saira:2.646874,Scomberesox_saurus:2.646874):16.121785):1.508349):3.721938):5.88654):2.878009):14.301133,((Arrhamphus_sclerolepis:24.704904,(Hyporhamphus_affinis:1.178428,Hyporhamphus_dussumieri:1.178428):23.526476):12.189109,((Hemiramphus_brasiliensis:13.392495,Oxyporhamphus_micropterus:13.392495):10.26042,(Parexocoetus_brachypterus:18.641912,((Cypselurus_callopterus:6.414034,Exocoetus_monocirrhus:6.414034):4.606228,((Cheilopogon_pinnatibarbatus:8.078435,Cheilopogon_melanurus:8.078435):1.264667,(Hirundichthys_marginatus:7.633585,(Cheilopogon_dorsomacula:3.938268,Prognichthys_brevipinnis:3.938268):3.695317):1.709517):1.67716):7.62165):5.011003):13.241098):10.170615):24.814413)Beloniformes:4.522564):0.998395)Atherinomorphae:17.246074):2.573621,(((Parambassis_ranga:4.300467,Ambassis_urotaenia:4.300467):42.908908,(Ambassis_agrammus:37.721223,Ambassis_interrupta:37.721223):9.488152):47.378136,(((Halidesmus_scapularis:19.129654,(Congrogadus_subducens:12.423811,Natalichthys_sam:12.423811):6.705843):65.72699,((Parma_microlepis:29.067354,(((Plectroglyphidodon_johnstonianus:8.386886,Plectroglyphidodon_dickii:8.386886):9.65747,(Hypsypops_rubicundus:12.304306,(Microspathodon_chrysurus:6.881828,Microspathodon_bairdii:6.881828):5.422478):5.74005):5.039146,(Stegastes_albifasciatus:21.575703,(Lepidozygus_tapeinosoma:19.961142,(Stegastes_partitus:10.740451,(Stegastes_fuscus:3.606957,Stegastes_diencaeus:3.606957):7.133494):9.220691):1.614561):1.507799):5.983852):6.532645,(((Chromis_atripectoralis:23.92163,(Chromis_cyanea:19.668093,Azurina_hirundo:19.668093):4.253537):2.560879,(Chromis_dimidiata:21.589296,(Dascyllus_aruanus:10.42299,(Dascyllus_carneus:5.674743,(Dascyllus_reticulatus:3.294907,Dascyllus_trimaculatus:3.294907):2.379836):4.748247):11.166306):4.893213):5.996685,((Abudefduf_saxatilis:8.193306,(Abudefduf_vaigiensis:6.153846,Abudefduf_sexfasciatus:6.153846):2.03946):23.164854,(Chrysiptera_taupou:23.043912,((Dischistodus_perspicillatus:16.667977,Pomachromis_richardsoni:16.667977):4.069637,(Amphiprion_ocellaris:19.611053,(((Amblyglyphidodon_leucogaster:14.024721,Acanthochromis_polyacanthus:14.024721):1.281718,(Neoglyphidodon_polyacanthus:11.183065,Neoglyphidodon_melas:11.183065):4.123374):2.967532,((Neopomacentrus_cyanomos:16.106197,Amphiprion_clarkii:16.106197):1.301497,(Pomacentrus_brachialis:11.482593,(Pomacentrus_spilotoceps:10.044386,Pomacentrus_pavo:10.044386):1.438207):5.925101):0.866277):1.337082):1.126561):2.306298):8.314248):1.121034):3.120805):49.256645):8.186887,(((Amphistichus_argenteus:7.3609,Hyperprosopon_anale_argenteum:7.3609):5.12006,(Cymatogaster_aggregata:9.498888,((Embiotoca_jacksoni:4.621261,Embiotoca_lateralis:4.621261):1.152342,(Zalembius_rosaceus:3.479384,(Phanerodon_furcatus:2.729151,Rhacochilus_vacca:2.729151):0.750233):2.294219):3.725285):2.982072):79.054345,((Neomyxus_leuciscus:45.332456,((Mugil_curema:21.429647,(Mugil_cephalus:19.263361,Mugil_trichodon:19.263361):2.166286):15.095634,((Moolgarda_engeli:15.623766,(Valamugil_buchanani:7.258517,Crenimugil_crenilabis:7.258517):8.365249):10.899382,(Myxus_capensis:20.370079,(Liza_richardsonii:11.151445,Chelon_macrolepis:11.151445):9.218634):6.153069):10.002133):8.807175)Mugiliformes:44.431485,((Lipogramma_trilineata:30.399056,Lipogramma_anabantoides:30.399056):57.64089,((Plesiops_coeruleolineatus:7.580044,Plesiops_melas:7.580044):79.404154,((Pseudoplesiops_revellei:60.598835,((Ogilbyina_novaehollandiae:22.700357,Labracinus_cyclophthalmus:22.700357):2.267877,(Pholidochromis_cerasina:20.528889,(Pseudochromis_fridmani:15.807128,(Pseudochromis_jamesi:14.334036,Pseudochromis_cyanotaenia:14.334036):1.473092):4.721761):4.439345):35.630601):25.023364,(Gramma_loreto:81.164935,((Opistognathus_maxillosus:33.277138,(Opistognathus_aurifrons:26.588425,Lonchopisthus_micrognathus:26.588425):6.688713):45.925,((((Lepadichthys_lineatus:17.336596,Diademichthys_lineatus:17.336596):20.225914,(Arcos_sp:18.655154,Gobiesox_maeandricus:18.655154):18.907356):35.987836,((Enneanectes_altivelis:31.556734,Enneanectes_boehlkei:31.556734):24.338998,(Enneapterygius_gruschkai:48.526856,(Enneapterygius_abeli:26.039104,(Helcogramma_ellioti_sp:11.052312,Helcogramma_fuscopinna:11.052312):14.986792):22.487752):7.368876):17.654614):3.123025,(((Gibbonsia_metzi:32.42937,((Pavoclinus_profundus:3.311804,Blennophis_striatus:3.311804):5.261594,(Clinus_cottoides:7.813834,(Clinus_superciliosus:5.776931,Muraenoclinus_dorsalis:5.776931):2.036903):0.759564):23.855972):18.31495,((((Stathmonotus_stahli:34.294766,Paraclinus_marmoratus:34.294766):8.524384,(Platygillellus_rubrocinctus:33.273043,Gillellus_semicinctus:33.273043):9.546107):2.824818,((Acanthemblemaria_paula:10.291854,Acanthemblemaria_aspera:10.291854):11.643632,(Emblemaria_pandionis:16.274634,(Lucayablennius_zingaro:10.917724,Chaenopsis_sp_alepidota:10.917724):5.35691):5.660852):23.708482):2.401714,(Neoclinus_blanchardi:45.65764,((Starksia_atlantica:20.906785,(Starksia_fasciata:15.54431,Starksia_ocellata:15.54431):5.362475):21.54664,((Labrisomus_multiporosus:23.811556,Labrisomus_nigricinctus:23.811556):11.340578,(Labrisomus_bucciferus:30.847081,(Malacoctenus_aurolineatus:19.434339,Malacoctenus_triangulatus:19.434339):11.412742):4.305053):7.301291):3.204215):2.388042):2.698638):17.52193,((Ecsenius_midas:20.757533,(Ecsenius_pardus:9.330095,Ecsenius_opsifrontalis:9.330095):11.427438):26.44987,(((Hypleurochilus_sp:28.590185,Hypsoblennius_hentz:28.590185):8.588366,(Enchelyurus_flavipes:35.153742,(Petroscirtes_mitratus:20.738729,(Meiacanthus_oualanensis_grammistes:18.49006,(Plagiotremus_rhinorhynchos:12.234118,Plagiotremus_tapeinosoma:12.234118):6.255942):2.248669):14.415013):2.024809):6.428789,((Cirripectes_stigmaticus:23.977773,(Ophioblennius_atlanticus:21.259299,(Cirripectes_quagga:16.143896,(Cirripectes_castaneus:12.588225,Cirripectes_filamentosus:12.588225):3.555671):5.115403):2.718474):13.192955,((Stanulus_sp:27.293598,(Alticus_arnoldorum:21.373525,(Nannosalarias_nativitatis:16.616851,(Salarias_fasciatus:4.970758,Atrosalarias_fuscus:4.970758):11.646093):4.756674):5.920073):3.750936,(Praealticus_caesius:21.121348,((Entomacrodus_nigricans:6.651164,(Entomacrodus_striatus:2.935441,Entomacrodus_niuafoouensis:2.935441):3.715723):12.782291,((Blenniella_cyanostigma:1.150842,Blenniella_chrysospilos_paula:1.150842):14.096808,(Ecsenius_bicolor:10.039814,(Istiblennius_dussumieri:5.159784,Blenniella_paula:5.159784):4.88003):5.207836):4.185805):1.687893):9.923186):6.126194):6.436612):3.600063):21.058847):8.407121)Blenniiformes:2.528767):1.962797):4.457264):1.361999):1.055748):1.723995):1.771364):1.508226):1.54398):2.632184)Ovalentaria:11.230458):3.449148,(((Gerres_oyena:31.967153,Eugerres_plumieri:31.967153):13.214677,(Gerres_longirostris:33.538035,(Gerres_cinereus:25.835379,(Ulaema_lefroyi:12.216435,(Eucinostomus_argenteus:8.877131,Eucinostomus_gula:8.877131):3.339304):13.618944):7.702656):11.643795):59.618171,((Champsodon_snyderi:93.628367,((Lachnolaimus_maximus:59.825024,(Haletta_semifasciata:53.314716,(Decodon_puellaris:42.908596,(Clepticus_parrae:33.343855,(Bodianus_mesothorax:11.194671,Bodianus_axillaris:11.194671):22.149184):9.564741):10.40612):6.510308):16.825549,(((Novaculichthys_taeniourus:25.653416,Xyrichtys_novacula_martinicensis:25.653416):31.457367,(Cheilio_inermis:53.277111,((Stethojulis_balteata:9.983011,Stethojulis_strigiventer:9.983011):28.997049,((Hologymnosus_doliatus:21.754371,(Coris_caudimacula:15.91273,(Coris_gaimard:8.042665,Coris_formosa:8.042665):7.870065):5.841641):12.40746,(Anampses_lineatus:32.174586,(((Halichoeres_bathyphilus_bivittatus:17.045337,Oxyjulis_californica:17.045337):10.479954,((Labropsis_australis:6.534163,Diproctacanthus_xanthurus:6.534163):12.166505,(Labrichthys_unilineatus:16.11964,Labroides_dimidiatus:16.11964):2.581028):8.824623):1.889232,((Thalassoma_quinquevittatum:7.827371,(Gomphosus_varius:5.806934,(Thalassoma_lunare:3.528429,Thalassoma_amblycephalum:3.528429):2.278505):2.020437):19.363015,((Coris_batuensis:9.160764,Halichoeres_margaritaceus:9.160764):10.736811,(Macropharyngodon_bipartitus:19.739067,(Halichoeres_biocellatus:8.937511,Halichoeres_iridis:8.937511):10.801556):0.158508):7.292811):2.224137):2.760063):1.987245):4.818229):14.297051):3.833672):12.229296,((Pteragogus_enneacanthus:50.69613,((Cirrhilabrus_punctatus:8.392353,Cirrhilabrus_katherinae:8.392353):34.405461,(Pseudocheilinus_evanidus:27.752423,Pseudocheilinus_hexataenia:27.752423):15.045391):7.898316):16.356272,((Tautoga_onitis:13.055908,Tautogolabrus_adspersus:13.055908):48.597667,(((Cheilinus_chlorourus:8.409669,Cheilinus_oxycephalus:8.409669):16.243577,(Epibulus_insidiator:21.250317,((Cheilinus_fasciatus:14.720749,Wetmorella_nigropinnata:14.720749):1.353183,(Oxycheilinus_celebicus:10.10906,(Oxycheilinus_digramma:6.555915,Oxycheilinus_unifasciatus:6.555915):3.553145):5.964872):5.176385):3.402929):33.256324,(Calotomus_carolinus:41.935106,(Cryptotomus_roseus:36.557555,(Hipposcarus_longiceps:26.519779,((Leptoscarus_vaigiensis:18.783016,(Sparisoma_aurofrenatum:5.081416,(Sparisoma_viride:2.797865,Sparisoma_chrysopterum:2.797865):2.283551):13.7016):4.368826,(Cetoscarus_bicolor:19.398126,(Chlorurus_sordidus:12.004268,((Scarus_quoyi:6.267289,Scarus_globiceps:6.267289):3.392749,((Scarus_iseri:6.876703,Scarus_rubroviolaceus:6.876703):1.069357,(Scarus_niger:7.190229,(Chlorurus_gibbus:5.467856,Scarus_ghobban:5.467856):1.722373):0.755831):1.713978):2.34423):7.393858):3.753716):3.367937):10.037776):5.377551):15.974464):3.744005):5.398827):2.287677):7.310494)Labriformes:16.977794):2.671634,((((Drepane_punctata:67.659163,(Chaetodipterus_faber:32.17985,(Platax_orbicularis:9.449899,Platax_teira:9.449899):22.729951):35.479313)Ephippiformes:20.887791,(Dicentrarchus_labrax:22.857155,(Morone_saxatilis:11.716263,(Morone_chrysops:10.272233,(Morone_mississippiensis:6.345988,Morone_americana:6.345988):3.926245):1.44403):11.140892):65.689799):5.265504,((((Datnioides_microlepis:21.631947,Lobotes_surinamensis:21.631947):64.806165,((Menticirrhus_undulatus_littoralis:8.847711,Menticirrhus_saxatilis:8.847711):22.317433,(Leiostomus_xanthurus:27.172082,(Aplodinotus_grunniens:26.095556,((Micropogonias_undulatus:17.304015,Sciaenops_ocellatus:17.304015):7.946327,(Pogonias_cromis:24.82357,((Atractoscion_nobilis:15.728504,(Cynoscion_regalis:4.188845,Cynoscion_arenarius:4.188845):11.539659):8.366952,((Seriphus_politus:18.535475,Genyonemus_lineatus:18.535475):4.455071,((Cheilotrema_saturnum:6.824782,(Pareques_acuminatus:3.861454,(Umbrina_coroides:2.709683,Pareques_umbrosus:2.709683):1.151771):2.963328):13.894662,(Larimus_breviceps:19.578428,(Stellifer_lanceolatus:13.624846,(Bairdiella_chrysoura:10.836817,(Odontoscion_dentex:7.01052,Corvula_sanctaeluciae:7.01052):3.826297):2.788029):5.953582):1.141016):2.271102):1.10491):0.728114):0.426772):0.845214):1.076526):3.993062):55.272968):5.761888,(((Monodactylus_sebae:18.728404,Monodactylus_argenteus:18.728404):51.604917,(Luvarus_imperialis:60.6,(Zanclus_cornutus:55.859027,((Naso_brevirostris:5.919136,(Naso_lituratus:4.137331,Naso_unicornis:4.137331):1.781805):44.080864,((Paracanthurus_hepatus:14.137121,(Zebrasoma_velifer:10.236227,(Zebrasoma_flavescens:2.172828,(Zebrasoma_scopas:1.504106,Zebrasoma_rostratum:1.504106):0.668722):8.063399):3.900894):23.966663,((Acanthurus_bahianus:12.952464,(Ctenochaetus_striatus:11.352594,(Ctenochaetus_strigosus:6.829836,Ctenochaetus_truncatus:6.829836):4.522758):1.59987):2.132435,((Acanthurus_guttatus:11.240187,Acanthurus_leucosternon:11.240187):2.085223,(Acanthurus_lineatus:12.480612,Acanthurus_triostegus:12.480612):0.844798):1.759489):23.018885):11.896216):5.859027):4.740973)Acanthuriformes:9.733321):15.366679,(((Chaetodontoplus_melanosoma:29.920716,(((Pomacanthus_imperator:8.009565,Pomacanthus_semicirculatus:8.009565):5.376668,(Pomacanthus_zonipectus:5.78846,Pomacanthus_arcuatus:5.78846):7.597773):9.102652,((Holacanthus_tricolor:7.270008,(Holacanthus_passer:2.417295,Holacanthus_ciliaris:2.417295):4.852713):7.614042,(Pygoplites_diacanthus:13.852988,(Apolemichthys_trimaculatus:12.573952,(Centropyge_loricula:11.689972,(Centropyge_nox:4.036768,Centropyge_bicolor:4.036768):7.653204):0.88398):1.279036):1.031062):7.604835):7.431831):24.513555,((Gazza_minuta:14.8,Leiognathus_equulus:14.8):17.9,((Chelmon_rostratus:18.185276,(Forcipiger_flavissimus:9.806327,(Hemitaurichthys_polylepis:8.395974,(Heniochus_varius:5.912112,(Johnrandallia_nigrirostris:5.885157,Heniochus_chrysostomus:5.885157):0.026955):2.483862):1.410353):8.378949):1.996908,(Prognathodes_aya_aculeatus:8.3,((Chaetodon_plebeius:4.822393,(Chaetodon_ornatissimus:0.647579,Chaetodon_reticulatus:0.647579):4.174814):1.936588,(Chaetodon_auriga:5.603651,(Chaetodon_ocellatus:4.267126,(Chaetodon_striatus:3.165069,Chaetodon_capistratus:3.165069):1.102057):1.336525):1.15533):1.541019):11.882184):12.517816):21.734271):17.438853,((Erythrocles_schlegelii:25.946762,Erythrocles_scintillans:25.946762):43.924992,((Malacanthus_plumieri:38.712662,(Caulolatilus_princeps:10.299787,Caulolatilus_intermedius:10.299787):28.412875):29.591099,(((Plectorhinchus_vittatus:10.298102,Plectorhinchus_chaetodonoides:10.298102):39.230988,(Orthopristis_chrysoptera:27.746908,((Pomadasys_corvinaeformis:22.298685,Conodon_nobilis:22.298685):3.955521,((Anisotremus_virginicus:15.942937,Anisotremus_surinamensis:15.942937):8.388909,(Xenistius_californiensis:17.305426,((Haemulon_aurolineatum:11.405403,Haemulon_vittatum:11.405403):2.384293,(Haemulon_sciurus:7.850719,Haemulon_plumierii:7.850719):5.938977):3.51573):7.02642):1.92236):1.492702):21.782182):15.070911,((Apsilus_dentatus:41.167776,(Aprion_virescens:33.250378,(Pristipomoides_aquilonaris:19.793317,(Pristipomoides_auricilla:17.471283,Aphareus_furca:17.471283):2.322034):13.457061):7.917398):7.62609,((Lutjanus_griseus:16.89237,(Lutjanus_biguttatus:15.1579,(Ocyurus_chrysurus:10.41623,(Lutjanus_campechanus:10.062818,(Lutjanus_mahogoni:9.547049,Rhomboplites_aurorubens:9.547049):0.515769):0.353412):4.74167):1.73447):7.100756,(Macolor_niger:15.308249,((Caesio_cuning:10.202961,Caesio_caerulaurea_lunaris:10.202961):1.961701,((Pterocaesio_tile:5.527611,Caesio_varilineata:5.527611):5.634724,(Pterocaesio_pisang:5.270243,(Caesio_teres:3.083941,Caesio_xanthonota:3.083941):2.186302):5.892092):1.002327):3.143587):8.684877):24.80074):15.806135):3.70376):1.567993):2.00137):13.826876):6.5):0.783285,(((Grammatonotus_surugaensis:77.124829,(Sillago_chondropus:32.79264,Sillago_sihama:32.79264):44.332189):8.728698,((Pentapodus_caninus:26.823386,(Scolopsis_frenata:18.47995,(Scolopsis_bilineata:14.853074,Scolopsis_margaritifera:14.853074):3.626876):8.343436):53.447398,(((Gymnocranius_grandoculis:16.945242,Monotaxis_grandoculis:16.945242):39.977364,(Lethrinus_erythropterus:18.973777,(Lethrinus_olivaceus:15.451662,(Lethrinus_harak:11.971663,(Lethrinus_obsoletus:6.184741,Lethrinus_atkinsoni:6.184741):5.786922):3.479999):3.522115):37.948829):17.448188,((Pagrus_pagrus:18.954067,Argyrozona_argyrozona:18.954067):11.722204,((Acanthopagrus_catenula:17.12786,(Sarpa_salpa:12.407865,Diplodus_capensis:12.407865):4.719995):9.075531,((Lagodon_rhomboides:18.278609,Archosargus_probatocephalus:18.278609):2.199256,(Stenotomus_chrysops:17.343404,(Calamus_penna:9.124937,Calamus_calamus:9.124937):8.218467):3.134461):5.725526):4.47288):43.694523):5.89999)Spariformes:5.582743):4.420399,((Siganus_spinus:19.354818,(Siganus_argenteus:15.111025,(Siganus_vulpinus:4.808076,(Siganus_stellatus:2.106997,Siganus_punctatus:2.106997):2.701079):10.302949):4.243793):65.776064,(((Scatophagus_argus:14.457935,Selenotoca_multifasciata:14.457935):61.402524,((Cepola_schlegelii:20.839671,Sphenanthias_tosaensis:20.839671):45.661543,(Pristigenys_alta:35.954641,(Priacanthus_arenatus:17.701916,Heteropriacanthus_cruentatus:17.701916):18.252725):30.546573):9.359245):5.908442,((Capros_aper:66.802727,(Antigonia_rubescens:10.905702,Antigonia_capros:10.905702):55.897025):13.997274,(((Lophiodes_reticulatus:22.462201,(Lophius_gastrophysus:2.495452,Lophius_americanus:2.495452):19.966749):42.032117,((Fowlerichthys_radiosus:30.458137,(Histiophryne_cryptacanthus:27.013454,(Histrio_histrio:12.333108,(Antennatus_coccineus:10.534045,Antennatus_nummifer:10.534045):1.799063):14.680346):3.444683):15.341864,((Halieutichthys_aculeatus:21.203888,(Dibranchus_tremendus:17.846967,(Ogcocephalus_parvus_nasutus:0.862633,Ogcocephalus_radiatus:0.862633):16.984334):3.356921):23.262122,((Chaunax_suttkusi:5.449484,Chaunax_stigmaeus:5.449484):33.050089,((Gigantactis_sp:14.287816,(Gigantactis_vanhoeffeni:6.268163,Gigantactis_ios:6.268163):8.019653):18.623814,((Cryptopsaras_couesii:20.548717,(Ceratias_holboelli:2.995618,Ceratias_sp:2.995618):17.553099):10.41616,((Himantolophus_albinares_sagamius:14.456809,(Melanocetus_murrayi:2.918086,Melanocetus_johnsonii:2.918086):11.538723):9.124163,(Bertella_idiomorpha:16.387383,(Oneirodes_macrosteus:10.164362,(Oneirodes_bulbosus:4.568319,Dolopichthys_sp:4.568319):5.596043):6.223021):7.193589):7.383905):1.946753):5.587943):5.966437):1.333991):18.694317)Lophiiformes:15.895554,((Triodon_macropterus:75.474468,((Triacanthus_biaculeatus:64.492986,(Halimochirurgus_alcocki:21.780217,(Triacanthodes_anomalus:1.062324,Triacanthodes_ethiops:1.062324):20.717893):42.712769):10.123884,((Anoplocapros_lenticularis:9.298842,Aracana_aurita:9.298842):45.501158,(Ostracion_cubicus:40.906398,(Rhinesomus_triqueter:20.731735,Acanthostracion_quadricornis:20.731735):20.174663):13.893602):19.81687):0.857598):2.325533,(((Chilomycterus_schoepfii:12.19839,Diodon_holocanthus:12.19839):43.701611,((Tetractenos_hamiltoni:19.959527,Takifugu_rubripes:19.959527):15.640474,(Lagocephalus_laevigatus:34.623454,((Sphoeroides_nephelus:3.189226,Sphoeroides_maculatus:3.189226):29.531603,((Canthigaster_bennetti:10.228754,(Canthigaster_jactator:7.490666,Canthigaster_valentini:7.490666):2.738088):13.996958,((Arothron_hispidus:6.632535,Arothron_nigropunctatus:6.632535):13.663845,(Tetraodon_miurus:18.197952,(Tetraodon_fluviatilis:0.918738,Tetraodon_nigroviridis:0.918738):17.279214):2.098428):3.929332):8.495117):1.902625):0.976547):20.3):17.334862,((Ranzania_laevis:22.000001,(Mola_mola:9.255334,Masturus_lanceolatus:9.255334):12.744667):46.610273,(((Aluterus_scriptus:24.377014,(Amanses_scopas:11.327068,Cantherhines_pardalis_pullus:11.327068):13.049946):3.216101,(Oxymonacanthus_longirostris:26.823609,(Paraluteres_prionurus:22.166933,(Stephanolepis_hispidus:20.308774,(Pervagor_janthinosoma:15.394884,(Acreichthys_tomentosus:14.512206,Pervagor_nigrolineatus:14.512206):0.882678):4.91389):1.858159):4.656676):0.769506):16.206886,(((Pseudobalistes_flavimarginatus:9.839815,(Xanthichthys_ringens:3.788257,Xanthichthys_auromarginatus:3.788257):6.051558):6.146411,(Balistapus_undulatus:12.458223,(Balistoides_conspicillum:10.763366,(Melichthys_niger:4.645391,Melichthys_indicus:4.645391):6.117975):1.694857):3.528003):3.569786,((Pseudobalistes_fuscus:16.149258,(Balistes_vetula:11.073547,Balistes_capriscus:11.073547):5.075711):2.212859,(Canthidermis_maculata:18.117763,((Sufflamen_fraenatum:5.570154,Abalistes_stellatus:5.570154):12.129847,(Sufflamen_chrysopterum:15.515234,(Rhinecanthus_verrucosus:3.424718,(Rhinecanthus_assasi:2.297794,Rhinecanthus_aculeatus:2.297794):1.126924):12.090516):2.184767):0.417762):0.244354):1.193895):24.243989):24.810273):4.624589):4.565138)Tetraodontiformes:2.589871):0.410129):0.9689):3.361981):5.143044):2.709359):0.829173):1.980895,((Centrogenys_vaigiensis:89.029209,((Astroscopus_ygraecum:45.444573,(Uranoscopus_sulphureus:45.364025,(Kathetostoma_albigutta:6.141349,Kathetostoma_averruncus:6.141349):39.222676):0.080548):38.552254,((Ammodytes_dubius:4.401809,Ammodytes_hexapterus:4.401809):74.183219,(Cheimarrichthys_fosteri:72.832529,(Parapercis_punctulata:20.607195,(Parapercis_hexophtalma:10.938132,Parapercis_clathrata:10.938132):9.669063):52.225334):5.752499):5.411799)Uranoscopiformes:5.032382):6.241731,(((((Epigonus_pandionis:33.002561,Epigonus_telescopus:33.002561):53.144111,((Howella_brodiei:26.984078,Howella_zina:26.984078):55.835149,(Acropoma_japonicum:75.274939,Ostracoberyx_dorygenys:75.274939):7.544288):3.327445):3.497909,((Synagrops_bellus:36.307076,Synagrops_spinosus:36.307076):52.374034,((Malakichthys_elegans:82.997929,(Stereolepis_gigas:77.80727,(Lateolabrax_japonicus:70.780688,Polyprion_americanus:70.780688):7.026582):5.190659):4.901463,((Banjos_banjos:60.576642,(Histiopterus_typus:49.182805,(Pentaceros_japonicus:33.520619,(Pentaceros_wheeleri:31.203915,Pentaceros_pectoralis:31.203915):2.316704):15.662186):11.393837):26.783473,((Acanthaphritis_unoorum:66.166223,Limnichthys_sp:66.166223):18.796719,((Glaucosoma_buergeri:11.362664,Glaucosoma_hebraicum:11.362664):55.254693,(Parapriacanthus_ransonneti:44.085728,((Pempheris_schomburgkii:29.121414,Pempheris_schwenkii:29.121414):2.45015,(Pempheris_vanicolensis:3.428146,Pempheris_oualensis:3.428146):28.143418):12.514164):22.531629):18.345585):2.397173):0.539277):0.781718):0.963471)Pempheriformes:3.529907,((Girella_nigricans_mezina:73.558804,((Oplegnathus_punctatus:61.207262,(Kuhlia_rupestris:21.296641,(Kuhlia_mugil:17.371047,Kuhlia_marginata:17.371047):3.925594):39.910621):7.298334,((Terapon_jarbua:28.825085,(Hephaestus_fuliginosus:7.127721,Scortum_barcoo:7.127721):21.697364):34.976869,(Kyphosus_sectatrix:20.590539,(Kyphosus_incisor:10.664446,(Kyphosus_cinerascens:6.772866,Kyphosus_elegans:6.772866):3.89158):9.926093):43.211415):4.703642):5.053208)Terapontiformes:11.103907,((Macquaria_colonorum:7.18407,Macquaria_novemaculeata:7.18407):68.510836,((Maccullochella_peelii:51.757161,(Gadopsis_marmoratus:50.773244,((Nannoperca_australis:38.168409,Macquaria_ambigua:38.168409):3.948007,(Percichthys_trucha:18.997907,Percilia_irwini:18.997907):23.118509):8.656828):0.983917):17.94284,((((Amblycirrhitus_pinos:35.323278,Paracirrhites_forsteri_arcatus:35.323278):4.393797,(Neocirrhites_armatus:31.535456,(Cirrhitichthys_oxycephalus:20.902936,Cirrhitichthys_falco:20.902936):10.63252):8.181619):26.749986,((Cheilodactylus_fasciatus:22.013875,Cheilodactylus_pixi:22.013875):11.724293,(Cheilodactylus_variegatus:12.963263,(Chirodactylus_jessicalenorum:4.995569,Chirodactylus_brachydactylus:4.995569):7.967694):20.774905):32.728893):2.532124,((Enoplosus_armatus:51.893024,(Coreoperca_whiteheadi:38.15934,(Siniperca_scherzeri:7.973286,Siniperca_chuatsi:7.973286):30.186054):13.733684):11.154204,((Elassoma_okefenokee:9.831207,(Elassoma_evergladei:5.031386,Elassoma_zonatum:5.031386):4.799821):39.268794,(Acantharchus_pomotis:35.569279,((Pomoxis_nigromaculatus:16.7,(Archoplites_interruptus:15.292892,Ambloplites_rupestris:15.292892):1.407108):12.310412,(Micropterus_salmoides:24.739672,(Lepomis_macrochirus:9.083859,Lepomis_cyanellus:9.083859):15.655813):4.27074):6.558867):13.530722):13.947227):5.951957):0.700816):5.994905)Centrarchiformes:8.967805):8.511777):1.725513,(((Centropristis_striata:46.868256,(Paralabrax_nebulifer:37.52673,((Serranus_tigrinus:22.855237,Serranus_baldwini:22.855237):12.480224,(Hypoplectrus_puella:24.888476,((Diplectrum_formosum:0.700106,Diplectrum_bivittatum:0.700106):18.738279,(Serranus_notospilus:5.874997,Serranus_phoebe:5.874997):13.563388):5.450091):10.446985):2.191269):9.341526):33.250855,(((Liopropoma_mowbrayi:8.336871,Liopropoma_rubre:8.336871):59.844566,((Pseudanthias_squamipinnis:27.847937,Pseudanthias_pascalus:27.847937):7.275049,(Odontanthias_chrysostictus:30.856299,(Baldwinella_aureorubens:21.177277,(Baldwinella_vivana:13.154899,(Anthias_nicholsi:8.44807,Pronotogrammus_martinicensis:8.44807):4.706829):8.022378):9.679022):4.266687):33.058451):7.392005,(((Aporops_bilinearis:19.595822,Pseudogramma_polyacantha:19.595822):27.656961,((Rypticus_saponaceus:11.018604,Rypticus_subbifrenatus:11.018604):12.543979,(Grammistops_ocellatus:21.237152,Grammistes_sexlineatus:21.237152):2.325431):23.6902):19.590974,((Hyporthodus_flavolimbatus:17.216026,(Mycteroperca_bonaci_microlepis:14.018424,(Epinephelus_maculatus:9.679715,Epinephelus_merra:9.679715):4.338709):3.197602):13.920868,(Aethaloperca_rogaa:25.497843,(Cephalopholis_argus:20.000404,(Cephalopholis_fulva:14.49995,Cephalopholis_miniata:14.49995):5.500454):5.497439):5.639051):35.706863):8.729685):4.545669):2.08089,((Niphon_spinosus:66.034644,(((Perca_fluviatilis:26.565471,Perca_flavescens:26.565471):6.076088,(Sander_vitreus:20.44789,(Romanichthys_valsanicola:10.653018,(Zingel_zingel:8.54132,Zingel_streber:8.54132):2.111698):9.794872):12.193669):7.620138,((Gymnocephalus_cernuus:17.782765,Gymnocephalus_schraetser:17.782765):10.222622,(((Etheostoma_juliae:17.148898,Etheostoma_vitreum:17.148898):3.259541,(Etheostoma_zonale:14.408119,(Etheostoma_simoterum:1.030301,Etheostoma_atripinne:1.030301):13.377818):6.00032):2.94762,((Percina_caprodes:13.615157,(Percina_phoxocephala:11.718805,Percina_nigrofasciata:11.718805):1.896352):8.422575,(Crystallaria_asprella:18.728111,(Ammocrypta_beanii:10.972819,(Ammocrypta_meridiana:5.304536,Ammocrypta_pellucida:5.304536):5.668283):7.755292):3.309621):1.318327):4.649328):12.25631):25.772947):12.542662,(((Cottoperca_trigloides:32.48141,Bovichtus_diacanthus:32.48141):30.539844,(Pseudaphritis_urvillii:46.262203,(Eleginops_maclovinus:26.692961,(Aethotaxis_mitopteryx:11.515338,(Dissostichus_eleginoides:11.01354,((Patagonotothen_tessellata:6.247258,Pagothenia_borchgrevinki:6.247258):4.476855,(Gobionotothen_gibberifrons:10.30631,(Notothenia_coriiceps:9.671118,((Harpagifer_antarcticus:6.338216,(Artedidraco_orianae:2.348106,Pogonophryne_barsukovi:2.348106):3.99011):1.076471,(Gymnodraco_acuticeps:6.79299,(Parachaenichthys_charcoti:6.390345,(Chionodraco_rastrospinosus:1.867689,Chionobathyscus_dewitti:1.867689):4.522656):0.402645):0.621697):2.256431):0.635192):0.417803):0.289427):0.501798):15.177623):19.569242):16.759051):12.936898,(((Bembras_japonica:49.422473,Parabembras_curtus:49.422473):19.932841,(((Bembrops_gobioides:4.349162,Bembrops_anatirostris:4.349162):58.182241,((Peristedion_ecuadorense:22.894708,(Peristedion_truncatum:9.471985,Peristedion_gracile:9.471985):13.422723):31.638001,(Pterygotrigla_hemisticta:41.909694,(Bellator_militaris:29.437262,(Prionotus_carolinus:18.132099,(Prionotus_evolans:4.835825,Prionotus_stephanophrys:4.835825):13.296274):11.305163):12.472432):12.623015):7.998694):3.954878,((Synanceia_verrucosa:22.624589,Coccotropsis_gymnoderma:22.624589):39.886512,((Scorpaenodes_guamensis:26.552475,(Scorpaenodes_albaiensis:24.974821,((Pterois_antennata:7.017601,Pterois_radiata:7.017601):0.638804,(Dendrochirus_zebra:5.919494,Pterois_miles:5.919494):1.736911):17.318416):1.577654):19.705166,(((Sebastolobus_alascanus:4.444486,Adelosebastes_latens:4.444486):30.466055,(Helicolenus_dactylopterus:15.754405,((Sebastes_paucispinis:9.408429,Sebastes_jordani:9.408429):1.21622,((Sebastes_aurora:3.496853,Sebastes_diploproa:3.496853):1.244081,(Sebastes_ruberrimus:4.274649,Sebastes_fasciatus:4.274649):0.466285):5.883715):5.129756):19.156136):8.779324,((Setarches_guentheri:33.436106,(Neomerinthe_hemingwayi:20.484462,(Pontinus_rathbuni:3.853914,Pontinus_longispinis:3.853914):16.630548):12.951644):6.678922,((Iracundus_signifer:23.086785,(Sebastapistes_cyanostigma:20.617551,(Caracanthus_maculatus:2.159477,Caracanthus_unipinna:2.159477):18.458074):2.469234):2.088979,((Taenianotus_triacanthus:18.953571,(Scorpaenopsis_longispina:8.125232,Scorpaenopsis_oxycephala:8.125232):10.828339):3.739619,((Scorpaena_brasiliensis:13.646687,Scorpaena_agassizii:13.646687):3.342477,(Scorpaena_guttata:7.421967,Scorpaena_dispar:7.421967):9.567197):5.704026):2.482574):14.939264):3.574837):2.567776):16.25346):3.97518):2.869033):3.752256,((Platycephalus_indicus:46.800937,(Rogadius_asper:27.226186,(Sunagocia_arenicola:5.504031,Thysanophrys_chiltonae:5.504031):21.722155):19.574751):23.994488,((Hoplichthys_langsdorfii:3.414302,Hoplichthys_gilberti:3.414302):62.659134,(Anoplopoma_fimbria:46.504651,((Rathbunella_hypoplecta:22.798585,((Bathymaster_caeruleofasciatus:5.087961,Bathymaster_signatus:5.087961):13.471246,(Cebidichthys_violaceus:15.585444,(Bryozoichthys_marjorius:14.216617,((Zoarces_americanus_viviparus:8.258259,(Lycenchelys_crotalinus:6.498597,(Bothrocara_hollandi:6.271915,(Lycodes_diapterus:5.824329,(Eucryphycus_californicus:5.439429,((Lycodapus_mandibularis:2.916574,Bothrocara_brunneum:2.916574):2.096831,(Melanostigma_pammelas:4.14763,(Lycodes_terraenovae:3.192163,Lycodes_brevipes:3.192163):0.955467):0.865775):0.426024):0.3849):0.447586):0.226682):1.759662):4.235336,((Anarrhichthys_ocellatus:3.233746,(Anarhichas_orientalis_lupus:1.992454,Anarhichas_denticulatus:1.992454):1.241292):4.696696,(Zaprora_silenus:7.397642,((Pholis_ornata:2.250673,Pholis_crassispina:2.250673):4.632989,(Cryptacanthodes_maculatus:6.26139,(Poroclinus_rothrocki:5.349006,(Leptoclinus_maculatus:3.948126,(Lumpenus_lampretaeformis:3.933508,Lumpenus_fabricii:3.933508):0.014618):1.40088):0.912384):0.622272):0.51398):0.5328):4.563153):1.723022):1.368827):2.973763):4.239378):19.028762,(((Aulorhynchus_flavidus:25.280384,(Hypoptychus_dybowskii:22.287004,Aulichthys_japonicus:22.287004):2.99338):1.019617,((Culaea_inconstans:19.844902,(Apeltes_quadracus:17.136647,Spinachia_spinachia:17.136647):2.708255):1.782128,(Pungitius_pungitius:16.827668,(Gasterosteus_aculeatus:8.991218,Gasterosteus_wheatlandi:8.991218):7.83645):4.799362):4.672971):13.534822,(Zaniolepis_frenata:33.581561,((Pleurogrammus_monopterygius:9.941558,(Hexagrammos_lagocephalus_otakii:4.4984,Hexagrammos_decagrammus:4.4984):5.443158):17.877416,((Trichodon_trichodon:22.810058,((Eumicrotremus_orbis:9.248856,Cyclopterus_lumpus:9.248856):11.51354,((Liparis_pulchellus:8.310921,Liparis_gibbus:8.310921):3.161614,((Careproctus_rastrinus:5.256799,Careproctus_melanurus:5.256799):4.213251,(Rhinoliparis_barbulifer:7.043116,(Paraliparis_copei:6.145461,(Paraliparis_hystrix:4.676096,Paraliparis_beani:4.676096):1.469365):0.897655):2.426934):2.002485):9.289861):2.047662):1.989944,(((Artediellus_uncinatus:16.740687,Scorpaenichthys_marmoratus:16.740687):2.351409,((Hypsagonus_quadricornis:14.409019,(Hemilepidotus_jordani:3.585276,Hemilepidotus_zapus:3.585276):10.823743):0.867894,((Sarritor_frenatus:4.982991,Sarritor_leptorhynchus:4.982991):5.478246,(Aspidophoroides_monopterygius:8.936652,(Stellerina_xyosterna:7.668274,(Bathyagonus_alascanus:5.475611,(Xeneretmus_latifrons:3.25175,Bathyagonus_pentacanthus:3.25175):2.223861):2.192663):1.268378):1.524585):4.815676):3.815183):1.279292,(Cottus_carolinae:18.193597,((Rastrinus_scutiger:12.737968,(Chitonotus_pugetensis:11.273779,(Icelinus_filamentosus:3.107033,Icelinus_quadriseriatus:3.107033):8.166746):1.464189):2.594817,((Gymnocanthus_galeatus:12.232601,Leptocottus_armatus:12.232601):2.628202,((Enophrys_taurina:11.853523,(Radulinus_asprellus:8.138826,(Myoxocephalus_octodecemspinosus:4.585021,(Microcottus_sellaris:3.25996,Myoxocephalus_polyacanthocephalus:3.25996):1.325061):3.553805):3.714697):2.17108,((Triglops_macellus:7.56846,Triglops_scepticus:7.56846):5.40511,(Dasycottus_setiger:10.723493,(Malacocottus_zonurus:10.180273,(Cottunculus_thomsonii:9.174171,Psychrolutes_phrictus:9.174171):1.006102):0.54322):2.250077):1.051033):0.8362):0.471982):2.860812):2.177791):4.428614):3.018972):5.762587):6.253262):1.992524):4.677304):19.568785):4.721989):2.312145):2.850582):2.619154):3.622695)Perciformes:12.7):0.370939):0.522413):0.506648):8.5)Eupercaria:7.0993):4.591565):5.109134):5.2):6.0)Percomorphaceae:12.2):1.463665)Euacanthomorphacea:8.336335):6.583092)Acanthomorphata:11.716908)Ctenosquamata:9.7):9.5)Neoteleostei:19.0):3.554892):16.945108)Euteleosteomorpha:18.8)Clupeocephala:23.2)Osteoglossocephalai:9.5)Teleostei:39.2)Neopterygii:27.6)Actinopteri:32.5)Actinopterygii:42.2)Osteichthyes:37.6,CHONDRICHTHYES@:462.4); diff --git a/dvc.lock b/dvc.lock index cc7581b..ce1c5f5 100644 --- a/dvc.lock +++ b/dvc.lock @@ -94,8 +94,8 @@ stages: deps: - path: data/OZTreeBuild/AllLife/BespokeTree/include_noAutoOTT/ hash: md5 - md5: 8cb57266b725e9893505618bf366af54.dir - size: 1231351 + md5: c3c1ebf2453c636e3ffdfcef58722d9c.dir + size: 1231291 nfiles: 56 params: params.yaml: @@ -104,8 +104,8 @@ stages: outs: - path: data/OZTreeBuild/AllLife/BespokeTree/include_OT_v16.1/ hash: md5 - md5: cfe57e6fbd3572028ac2d83203a96fe4.dir - size: 1534894 + md5: c12514e92740949250ecdb4375d6c360.dir + size: 1534814 nfiles: 55 get_open_trees_from_one_zoom: cmd: @@ -115,8 +115,8 @@ stages: deps: - path: data/OZTreeBuild/AllLife/BespokeTree/include_OT_v16.1/ hash: md5 - md5: cfe57e6fbd3572028ac2d83203a96fe4.dir - size: 1534894 + md5: c12514e92740949250ecdb4375d6c360.dir + size: 1534814 nfiles: 55 - path: data/OZTreeBuild/AllLife/OpenTreeParts/OT_required/ hash: md5 @@ -180,8 +180,8 @@ stages: deps: - path: data/OZTreeBuild/AllLife/BespokeTree/include_OT_v16.1/ hash: md5 - md5: cfe57e6fbd3572028ac2d83203a96fe4.dir - size: 1534894 + md5: c12514e92740949250ecdb4375d6c360.dir + size: 1534814 nfiles: 55 - path: data/OZTreeBuild/AllLife/OpenTreeParts/OpenTree_all/ hash: md5 @@ -254,8 +254,9 @@ stages: nfiles: 7 make_js_treefiles: cmd: - - mkdir -p data/js_output - - make_js_treefiles --outdir data/js_output + - rm -r data/js_output ; mkdir -p data/js_output + - make_js_treefiles --outdir data/js_output + data/output_files/ordered_tree_*.poly deps: - path: data/output_files/ hash: md5 diff --git a/dvc.yaml b/dvc.yaml index 94480a2..c3b4049 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -193,8 +193,11 @@ stages: make_js_treefiles: cmd: - - mkdir -p data/js_output - - make_js_treefiles --outdir data/js_output + - rm -r data/js_output ; mkdir -p data/js_output + - >- + make_js_treefiles + --outdir data/js_output + data/output_files/ordered_tree_*.poly deps: - data/output_files/ always_changed: true diff --git a/oz_tree_build/README.markdown b/oz_tree_build/README.markdown index 4f00d8d..cd5ca66 100755 --- a/oz_tree_build/README.markdown +++ b/oz_tree_build/README.markdown @@ -45,41 +45,6 @@ Then see the section titled "Upload data to the server and check it" below. Edit `params.yaml` to change the OpenTree version, taxonomy version, build version, etc. DVC will detect the parameter changes and re-run only the affected stages. -### Upload data to the server and check it - -8. If you are running the tree building scripts on a different computer to the one running the web server, you will need to push the `completetree_XXXXXX.js`, `completetree_XXXXXX.js.gz`, `cut_position_map_XXXXXX.js`, `cut_position_map_XXXXXX.js.gz`, `dates_XXXXXX.js`, `dates_XXXXXX.js.gz` files onto your server, e.g. by pushing to your local Github repo then pulling the latest github changes to the server. -1. (15 mins) load the CSV tables into the DB, using the SQL commands printed in step 6 (at the end of the `data/output_files/ordered_output.log` file: the lines that start something like `TRUNCATE TABLE ordered_leaves; LOAD DATA LOCAL INFILE ...;` `TRUNCATE TABLE ordered_nodes; LOAD DATA LOCAL INFILE ...;`). Either do so via a GUI utility, or copy the `.csv.mySQL` files to a local directory on the machine running your SQL server (e.g. using `scp -C` for compression) and run your `LOAD DATA LOCAL INFILE` commands on the mysql command line (this may require you to start the command line utility using `mysql --local-infile`, e.g.: - - ``` - mysql --local-infile --host db.MYSERVER.net --user onezoom --password --database onezoom_dev - ``` - -1. Check for dups, and if any sponsors are no longer on the tree, using something like the following SQL command: - - ``` - select * from reservations left outer join ordered_leaves on reservations.OTT_ID = ordered_leaves.ott where ordered_leaves.ott is null and reservations.verified_name IS NOT NULL; - select group_concat(id), group_concat(parent), group_concat(name), count(ott) from ordered_leaves group by ott having(count(ott) > 1) - ``` - -### Fill in additional server fields - -11. (15 mins) create example pictures for each node by percolating up. This requires the most recent `images_by_ott` table, so either do this on the main server, or (if you are doing it locally) update your `images_by_ott` to the most recent server version. - - ``` - ${OZ_DIR}/OZprivate/ServerScripts/Utilities/picProcess.py -v - ``` - -1. (5 mins) percolate the IUCN data up using - - ``` - ${OZ_DIR}/OZprivate/ServerScripts/Utilities/IUCNquery.py -v - ``` - - (note that this both updates the IUCN data in the DB and percolates up interior node info) - -1. (10 mins) If this is a site with sponsorship (only the main OZ site), set the pricing structure using SET_PRICES.html (accessible from the management pages). -1. (5 mins - this does seem to be necessary for ordered nodes & ordered leaves). Make sure indexes are reset. Look at `OZprivate/ServerScripts/SQL/create_db_indexes.sql` for the SQL to do this - this may involve logging in to the SQL server (e.g. via Sequel Pro on Mac) and pasting all the drop index and create index commands. - ### At last 15. Have a well deserved cup of tea diff --git a/oz_tree_build/taxon_mapping_and_popularity/CSV_base_table_creator.py b/oz_tree_build/taxon_mapping_and_popularity/CSV_base_table_creator.py index f968f7e..4581d7a 100755 --- a/oz_tree_build/taxon_mapping_and_popularity/CSV_base_table_creator.py +++ b/oz_tree_build/taxon_mapping_and_popularity/CSV_base_table_creator.py @@ -86,6 +86,7 @@ from dendropy import Node, Tree from ..images_and_vernaculars.get_wiki_images import get_qid_from_taxa_data +from ..utilities.debug_util import parse_args_and_add_logging_switch from ..utilities.file_utils import open_file_based_on_extension from . import OTT_popularity_mapping @@ -597,7 +598,6 @@ def output_simplified_tree(tree, taxonomy_file, outdir, version, seed, save_sql= set_node_ages, set_real_parent_nodes, write_brief_newick, - write_preorder_ages, write_preorder_to_csv, ) @@ -606,7 +606,6 @@ def output_simplified_tree(tree, taxonomy_file, outdir, version, seed, save_sql= Tree.prune_non_species = prune_non_species Tree.set_node_ages = set_node_ages Tree.set_real_parent_nodes = set_real_parent_nodes - Tree.write_preorder_ages = write_preorder_ages Tree.remove_unifurcations_keeping_higher_taxa = remove_unifurcations_keeping_higher_taxa Tree.write_preorder_to_csv = write_preorder_to_csv Tree.group_genera_in_polytomies = group_genera_in_polytomies @@ -664,8 +663,6 @@ def output_simplified_tree(tree, taxonomy_file, outdir, version, seed, save_sql= tree.seed_node.write_brief_newick(condensed_newick) with open(os.path.join(outdir, f"ordered_tree_{version}.poly"), "w+") as condensed_poly: tree.seed_node.write_brief_newick(condensed_poly, "{}") - with open(os.path.join(outdir, f"ordered_dates_{version}.js"), "w+") as json_dates: - tree.write_preorder_ages(json_dates, format="json") # these are the extra columns output to the leaf csv file leaf_extras = OrderedDict() @@ -720,19 +717,22 @@ def output_simplified_tree(tree, taxonomy_file, outdir, version, seed, save_sql= from shutil import copyfile from subprocess import call - # make CSV files that can be imported into mySQL (subs \\N for null values) - logging.info(" > saving extra file copies in mySQL format: import them using:") - for tab in ["_leaves", "_nodes"]: - fn = os.path.join(outdir, "ordered" + tab + f"_{version}" + ".csv") - sqlfile = fn + ".mySQL" - copyfile(fn, sqlfile) - call(["perl", "-pi", "-e", r"s/,(?=(,|\n))/,\\N/g", sqlfile]) - logging.info( - f"sql> TRUNCATE TABLE ordered{tab}; " - f"LOAD DATA LOCAL INFILE '{sqlfile}' REPLACE INTO TABLE `ordered{tab}` " - f"FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '\"' " - f"IGNORE 1 LINES ({open(fn).readline().rstrip()}) SET id = NULL;" - ) + with open(os.path.join(outdir, f"import_{version}.sql"), "w", encoding="utf-8") as sql_f: + # make CSV files that can be imported into mySQL (subs \\N for null values) + logging.info(" > saving extra file copies in mySQL format: import them using:") + for tab in ["_leaves", "_nodes"]: + fn = os.path.join(outdir, "ordered" + tab + f"_{version}" + ".csv") + sqlfile = fn + ".mySQL" + copyfile(fn, sqlfile) + call(["perl", "-pi", "-e", r"s/,(?=(,|\n))/,\\N/g", sqlfile]) + sql_f.writelines( + [ + f"TRUNCATE TABLE ordered{tab};\n" + f"LOAD DATA LOCAL INFILE '{sqlfile}' REPLACE INTO TABLE `ordered{tab}` \n" + f" FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '\"' \n" + f" IGNORE 1 LINES ({open(fn).readline().rstrip()}) SET id = NULL;\n" + ] + ) def display_WD_ott_stats(OTT_ptrs): @@ -940,12 +940,6 @@ def switch_otts_to_qids(taxa_data_file, tree): def process_all(args): random_seed_addition = 42 start = time.time() - if args.verbosity == 0: - logging.basicConfig(stream=sys.stderr, level=logging.WARNING) - elif args.verbosity == 1: - logging.basicConfig(stream=sys.stderr, level=logging.INFO, format="%(message)s") - elif args.verbosity >= 2: - logging.basicConfig(stream=sys.stderr, level=logging.DEBUG) logging.info(f"OneZoom data generation started on {time.asctime(time.localtime(time.time()))}") skip_popularity = ( args.popularity_file is None @@ -1138,15 +1132,8 @@ def main(): type=str, help="JSON file with persisted data about taxa, typically used for the extinct tree", ) - parser.add_argument( - "--verbosity", - "-v", - action="count", - default=0, - help="verbosity: output extra non-essential info", - ) - args = parser.parse_args() + args = parse_args_and_add_logging_switch(parser) process_all(args) diff --git a/oz_tree_build/taxon_mapping_and_popularity/dendropy_extras.py b/oz_tree_build/taxon_mapping_and_popularity/dendropy_extras.py index c1be404..cacdf5f 100755 --- a/oz_tree_build/taxon_mapping_and_popularity/dendropy_extras.py +++ b/oz_tree_build/taxon_mapping_and_popularity/dendropy_extras.py @@ -240,70 +240,6 @@ def remove_unifurcations_keeping_higher_taxa(self): return n_deleted -def write_preorder_ages(self, node_dates_fh, leaf_dates_fh=None, format="tsv"): # noqa A002 - """ - Write the dates to one or two files. If no second file is given, only write leaves if - the format is 'json'. The main file is for nodes: any absent dates should be treated - as unknown. The leaves file should be tiny: most leaves should not have a date, and - be treated as extant (0 Ma), unless they have an extinction_date set. - - Format can equal 'json', 'csv', or 'tsv' - """ - if format == "json": - start = "{" - end = ["}"] - sep = '":' - join = ['"', '"'] - - if format == "tsv": - sep = "\t" - end = [""] - start = "" - join = ["", ""] - - if format == "csv": - sep = "," - end = [""] - start = "" - join = ["", ""] - - leaf_num = 0 - node_num = 0 - if leaf_dates_fh or format == "json": - if leaf_dates_fh is None: - leaf_dates_fh = node_dates_fh - leaf_dates_fh.write('var tree_date = {"leaves":') - join = ['"', '"'] - end = ['},"nodes":', "}}"] - - leaf_dates_fh.write(start) - for leaf in self.leaf_node_iter(): - # for compactness, we should probably write this in binary, as a series of - # (4-byte int, float); for the moment write it as text format, to be gzipped - leaf_num += 1 - if (getattr(leaf, "age", None) is not None) and (leaf.age > 0): - leaf_dates_fh.write(join[0] + str(leaf_num) + sep + str(leaf.age)) - if format == "json": - # after first value, start putting initial commas (avoids trailing comma) - join[0] = ',"' - else: - join[0] = "\n" - leaf_dates_fh.write(end[0]) - leaf_dates_fh.flush() - - node_dates_fh.write(start) - for node in self.preorder_internal_node_iter(): - node_num += 1 - if getattr(node, "age", None) is not None: - node_dates_fh.write(join[-1] + str(node_num) + sep + str(node.age)) - if format == "json": - join[-1] = ',"' - else: - join[-1] = "\n" - node_dates_fh.write(end[-1]) - node_dates_fh.flush() - - def write_preorder_to_csv( self, leaf_file, diff --git a/oz_tree_build/tree_build/ott_mapping/add_ott_numbers_to_trees.py b/oz_tree_build/tree_build/ott_mapping/add_ott_numbers_to_trees.py index cd23e25..10025d1 100755 --- a/oz_tree_build/tree_build/ott_mapping/add_ott_numbers_to_trees.py +++ b/oz_tree_build/tree_build/ott_mapping/add_ott_numbers_to_trees.py @@ -22,7 +22,9 @@ """ # noqa E501 import argparse +import collections import json +import logging import os import re import sys @@ -31,6 +33,8 @@ from dendropy import Tree +logger = logging.getLogger(__name__) + unambiguous = 0 synonyms = 0 unidentified = 0 @@ -318,6 +322,9 @@ def lookup_OTT(name_node_dict, context): if len(remainder): names = [(n.label).replace("_", " ") for n in remainder] + duplicates = [item for item, count in collections.Counter(names).items() if count > 1] + if len(duplicates) > 0: + logging.error(f"File {f} has multiple nodes labelled: {duplicates}") lookup_OTT(dict(zip(names, remainder)), context_name) if args.savein: diff --git a/oz_tree_build/utilities/debug_util.py b/oz_tree_build/utilities/debug_util.py index e876e20..cea334d 100644 --- a/oz_tree_build/utilities/debug_util.py +++ b/oz_tree_build/utilities/debug_util.py @@ -1,9 +1,45 @@ +import atexit import logging +import os import sys -# Helper function to set up logging +class _ErrorCountingHandler(logging.Handler): + """Logging handler that counts records at ERROR level and above.""" + + def __init__(self): + super().__init__(level=logging.ERROR) + self.error_count = 0 + + def emit(self, record): + self.error_count += 1 + + +_error_handler = None + + +def _exit_if_errors_logged(): + # Raising SystemExit from an atexit hook does not propagate the exit code + # in Python 3, so we have to flush manually and call os._exit. By the time + # this runs (atexit fires in LIFO order, after main()'s normal return) + # the script's own output is already on disk; only logging buffers remain. + if _error_handler.error_count > 0: + logging.shutdown() + sys.stderr.write(f"Exiting with status 1: {_error_handler.error_count} error(s) were logged\n") + sys.stderr.flush() + sys.stdout.flush() + os._exit(1) + + def parse_args_and_add_logging_switch(parser): + """Add a ``--verbosity`` switch to ``parser``, parse args, configure logging. + + Also installs a handler on the root logger that counts ERROR-level records, + and an :mod:`atexit` hook that exits with status 1 if any were emitted, so + that logged errors propagate as a non-zero process exit status. + """ + global _error_handler + parser.add_argument( "--verbosity", "-v", @@ -21,4 +57,9 @@ def parse_args_and_add_logging_switch(parser): elif args.verbosity == 2: logging.basicConfig(stream=sys.stderr, level=logging.DEBUG) + if _error_handler is None: + _error_handler = _ErrorCountingHandler() + logging.getLogger().addHandler(_error_handler) + atexit.register(_exit_if_errors_logged) + return args diff --git a/oz_tree_build/utilities/make_js_treefiles.py b/oz_tree_build/utilities/make_js_treefiles.py index 9e8326b..fb33af2 100755 --- a/oz_tree_build/utilities/make_js_treefiles.py +++ b/oz_tree_build/utilities/make_js_treefiles.py @@ -2,28 +2,11 @@ import fileinput import json import os +import re import shutil from subprocess import call - -# argparse -> boolean -# produces true if all parameters are valid. -# print error message if: -# -- newick file can't be found -# -> can't find newick file: + file path -# -- completetree file dir not exist -# -> Output directory for completetree does not exist: + path -# -- cut_position_map file dir not exist -# -> Output directory for cut_position_map does not exist: + path -def parameter_valid(args): - parameter_valid = True - if not os.path.isfile(args.npath): - print("Can't find newick file: '" + args.npath + "'") - parameter_valid = False - if not os.path.exists(args.outdir): - print("Output directory does not exist: '" + args.outdir + "'") - parameter_valid = False - return parameter_valid +from ..utilities.debug_util import parse_args_and_add_logging_switch # string -> string @@ -157,6 +140,47 @@ def get_polytomy_substring_pos(start, end, start_end_arr, threshold, newick_str, return res +def write_js_file(outdir, input_path, version_number, args): + # Output to versioned path + input_name = os.path.basename(input_path) + output_path = os.path.join( + outdir, + re.sub( + # Extract any existing version number / extension from filename + r"(_\d+)?(\.[a-zA-Z]+)$", + # Replace with verison number / extension + "_" + str(version_number) + r"\2", + input_name, + ), + ) + + if input_name.startswith("ordered_tree_"): + output_path = re.sub(r"ordered_tree_", "completetree_", output_path) + output_path = re.sub(r"\.(nwk|poly)$", ".js", output_path) + + print(f"{input_path} -> {output_path}") + newick_str = tidy_newick(input_path) + with open(output_path, "w") as out_f: + out_f.write(generate_completetree_js(newick_str)) + + # Generate derived cut-position-map + cut_path = re.sub(r"completetree_", r"cut_position_map_", output_path) + with open(cut_path, "w") as out_f: + out_f.write(generate_cut_position_map(newick_str, args.threshold)) + # Trigger write_js_file for cut map so we gzip it + write_js_file(outdir, cut_path, version_number, args) + + elif input_path == output_path: + # Nothing to do, already in output_path + pass + else: + # By default we just copy file + print(f"{input_path} -> {output_path}") + shutil.copyfile(input_path, output_path) + print(f"{output_path} -> {output_path}.gz") + call(["gzip", "-9fk", output_path]) + + def main(): # rawData string + metadata -> output result into file. @@ -167,27 +191,8 @@ def main(): ) # pick the most recent ordered_tree_XXX.nwk file - import glob import re - datafile_name = "ordered_{data}_{version}.{ext}" - input_file = glob.glob( - os.path.join( - os.path.dirname(__file__), - "..", - "..", - "data", - "output_files", - datafile_name.format(data="tree", version="*", ext="poly"), - ) - ) - parser.add_argument( - "--npath", - default=input_file, - nargs="+", - help="filepath of polytomy-marked newick string", - ) - parser.add_argument( "--outdir", "-o", @@ -203,70 +208,40 @@ def main(): ), help="output filepath of cut_position_map", ) - parser.add_argument( - "--treefilename", - default="completetree_{version}.js", - help="output filepath of rawData and metadata", - ) - - parser.add_argument( - "--cutfilename", - default="cut_position_map_{version}.js", - help="output filepath of cut_position_map", - ) - - parser.add_argument( - "--datefilename", - default="dates_{version}.js", - help=( - "output filepath of json dates file (copied from " - + datafile_name.format(data="dates", version="XXXXX", ext="js") - + "in the same dir as the treefile)" - ), + "in_files", + nargs="+", + metavar="FILE", + help="Files to move to outdir, with versions appended if not present", ) - parser.add_argument( "--threshold", default=10000, type=int, help=("Threshold for deciding if a node and its descendants needs to be" "recorded in cut_position_map"), ) - - args = parser.parse_args() - # tidy up the file names to include versioning numbers - args.npath = max(args.npath, key=os.path.getctime) - version_number = re.search( - datafile_name.format(data="tree", version="([^/]+)", ext="(nwk|poly)"), - args.npath, - ).group(1) - print(f"Using version number: {version_number}") - treefile_path = os.path.join(args.outdir, args.treefilename.format(version=version_number)) - cutfile_path = os.path.join(args.outdir, args.cutfilename.format(version=version_number)) - datefile_inpath = os.path.join( - os.path.dirname(args.npath), - datafile_name.format(data="dates", version=version_number, ext="js"), + parser.add_argument( + "--version", + type=int, + help=("Version number / serial to append to file names, if not provided assume present on at least one file"), ) - datefile_outpath = os.path.join(args.outdir, args.datefilename.format(version=version_number)) - if parameter_valid(args): - newick_str = tidy_newick(args.npath) - treedata_str = generate_completetree_js(newick_str) - cutmap_str = generate_cut_position_map(newick_str, args.threshold) - with open(treefile_path, "w") as tree: - tree.write(treedata_str) - print("Generated file: " + treefile_path) - call(["gzip", "-9fk", treefile_path]) - print("Gzipped tree file") - with open(cutfile_path, "w") as cutfile: - cutfile.write(cutmap_str) - print("Generated file: " + cutfile_path) - call(["gzip", "-9fk", cutfile_path]) - print("Gzipped cutmap file") - print(f"Copying date file {datefile_inpath} to {datefile_outpath}") - shutil.copyfile(datefile_inpath, datefile_outpath) - call(["gzip", "-9fk", datefile_outpath]) - print("Gzipped date file") - print("Done") + + args = parse_args_and_add_logging_switch(parser) + + if args.version: + version_number = args.version + else: + # Find higest version number in files present, use that as version + version_number = 0 + for f in args.in_files: + m = re.search(r"_(\d+)\.(\w+)$", f) + if m and int(m.group(1)) > version_number: + version_number = int(m.group(1)) + + for f in args.in_files: + write_js_file(args.outdir, f, version_number, args) + + print("Done") if __name__ == "__main__": diff --git a/tests/test_debug_util.py b/tests/test_debug_util.py new file mode 100644 index 0000000..f1bf131 --- /dev/null +++ b/tests/test_debug_util.py @@ -0,0 +1,78 @@ +""" +Tests for parse_args_and_add_logging_switch. + +These spawn a subprocess for each case so we exercise the real atexit hook +and observe the actual process exit code, which is the whole point of the +helper. +""" + +import subprocess +import sys +import textwrap + + +def _run(body, *script_args): + """Run ``body`` under ``parse_args_and_add_logging_switch`` in a subprocess.""" + script = textwrap.dedent( + f""" + import argparse, logging + from oz_tree_build.utilities.debug_util import parse_args_and_add_logging_switch + parse_args_and_add_logging_switch(argparse.ArgumentParser()) + {body} + """ + ) + return subprocess.run( + [sys.executable, "-c", script, *script_args], + capture_output=True, + text=True, + ) + + +def test_no_logging_exits_zero(): + result = _run("pass") + assert result.returncode == 0 + assert "Exiting with status 1" not in result.stderr + + +def test_warning_only_exits_zero(): + result = _run("logging.warning('a warning')") + assert result.returncode == 0 + assert "a warning" in result.stderr + assert "Exiting with status 1" not in result.stderr + + +def test_logged_error_exits_one(): + result = _run("logging.error('boom')") + assert result.returncode == 1 + assert "boom" in result.stderr + assert "Exiting with status 1: 1 error(s) were logged" in result.stderr + + +def test_critical_counts_as_error(): + result = _run("logging.critical('fatal')") + assert result.returncode == 1 + assert "Exiting with status 1: 1 error(s) were logged" in result.stderr + + +def test_multiple_errors_counted(): + result = _run("logging.error('first'); logging.error('second')") + assert result.returncode == 1 + assert "Exiting with status 1: 2 error(s) were logged" in result.stderr + + +def test_verbose_flag_enables_info_output(): + result = _run("logging.info('hello info')", "-v") + assert result.returncode == 0 + assert "hello info" in result.stderr + + +def test_default_verbosity_suppresses_info(): + result = _run("logging.info('hello info')") + assert result.returncode == 0 + assert "hello info" not in result.stderr + + +def test_vv_enables_debug_output(): + result = _run("logging.debug('hello debug')", "-vv") + assert result.returncode == 0 + assert "hello debug" in result.stderr diff --git a/tests/test_files_felidae/expected_output_files_generation/ordered_dates_0.js b/tests/test_files_felidae/expected_output_files_generation/ordered_dates_0.js deleted file mode 100644 index 8278fe2..0000000 --- a/tests/test_files_felidae/expected_output_files_generation/ordered_dates_0.js +++ /dev/null @@ -1 +0,0 @@ -var tree_date = {"leaves":{},"nodes":{"1":13.882716,"2":12.358025,"3":10.191358,"4":12.197531,"5":8.265432,"6":6.5,"7":6.179012,"8":3.37037,"9":9.067901,"10":7.54321,"11":7.382716,"12":5.938272,"13":4.092593,"14":2.006173,"15":4.012346,"16":2.888889,"17":1.925926,"18":8.987654,"19":7.54321,"20":4.975309,"21":6.259259,"22":6.098765,"23":6.098765,"24":4.333333,"25":3.450617,"26":3.450617,"27":8.907407,"28":6.259259,"29":5.537037,"30":8.746913,"31":7.141975,"32":4.333333,"33":2.888889,"34":6.660493,"35":6.580246,"36":4.895061,"37":4.814814,"38":4.734567,"39":4.65432}} \ No newline at end of file