User:Jts1882/phylogeny/Fish Tree of Life

The Fish Tree of Life project provides downloadable Newick files for their order and family phylogenies. The cladograms on this page produced using the data in these files with the {{clade}} template and some regular expressions to trim the numerical information and add wikilinks.

Method

Uses the {{clade}} template with the |newickX= parameter to provide a Newick string. The parameters |newickX-patternY= and |newickX-replaceY= specify a pattern with a replacement string for preprocess the Newick string (X represents the number of the Newick string, Y the number of the operation to apply to that string). The first pattern and replacement remove the numbers after the colon. The second adds a wikilink to the taxon name.

{{clade
|newick1-pattern1=:[%d]+%.[%d]+
|newick1-replace1=
|newick1-pattern2=([%a]+)
|newick1-replace2=[[%1]]
|newick1=FISH_TREE_OF_LIFE_DATA
}}

Example using the order data:

{{clade
|newick1-pattern1=:[%d]+%.[%d]+
|newick1-replace1=
|newick1-pattern2=([%a]+)
|newick1-replace2=[[%1]]
|newick1=(Polypteriformes:368.027041,(Acipenseriformes:333.36982,((Lepisosteiformes:251.2,Amiiformes:251.2):48.943209,((Elopiformes:165.843139,(Anguilliformes:146.0535,(Notacanthiformes:128.347636,Albuliformes:128.347637):17.705862):19.789641):26.939643,((Osteoglossiformes:169.672422,Hiodontiformes:169.672422):17.471963,((Alepocephaliformes:171.108487,(Clupeiformes:165.805142,(Gonorynchiformes:158.176817,(Cypriniformes:142.110586,(Gymnotiformes:124.40688,(Siluriformes:116.06004,Characiformes:116.060038):8.346838):17.703708):16.06623):7.628325):5.303345):6.36875,(Lepidogalaxiiformes:172.157387,((Argentiniformes:158.384449,(Salmoniformes:121.520222,Esociformes:121.520223):36.864226):7.145808,((Stomiatiformes:141.207619,Osmeriformes:141.207618):20.672626,(Galaxiiformes:158.157427,(Ateleopodiformes:149.146565,(Aulopiformes:146.049394,(Myctophiformes:141.995558,((Polymixiiformes:125.926727,(Percopsiformes:119.550085,(Zeiformes:112.30372,(Gadiformes:99.890622,Stylephoriformes:99.890622):12.413099):7.246364):6.376642):12.033509,(Lampridiformes:135.505912,((Beryciformes:124.850407,Holocentriformes:124.850408):4.793566,(Ophidiiformes:122.65368,(Batrachoidiformes:120.167471,((Labriformes:112.838678,((Tetraodontiformes:101.62039,Lophiiformes:101.620388):4.659797,((Acanthuriformes:96.101473,Ephippiformes:96.101474):7.010952,(Spariformes:99.425522,(Incertae_sedis_in_Eupercaria:96.331828,(Uranoscopiformes:92.977695,(Perciformes:92.028374,(Centrarchiformes:90.740466,Pempheriformes:90.740464):1.287908):0.949321):3.354133):3.093696):3.686903):3.167759):6.558493):3.243613,(((Gobiiformes:99.575295,Kurtiformes:99.575295):11.781977,(Syngnathiformes:108.599677,Scombriformes:108.599675):2.757596):3.029696,(((Anabantiformes:94.89388,Synbranchiformes:94.89388):13.184223,((Pleuronectiformes:79.610542,Incertae_sedis_in_Carangaria:79.610542):3.123197,(Carangiformes:75.53813,Istiophoriformes:75.538129):7.195608):25.344365):5.14771,(Mugiliformes:107.660061,(Incertae_sedis_in_Ovalentaria:106.091317,((Cichliformes:98.738035,Pholidichthyiformes:98.738035):6.170613,(Atheriniformes:98.599758,(Cyprinodontiformes:97.3635,Beloniformes:97.363501):1.236257):6.308891):1.182668):1.568745):5.565751):1.161156):1.695324):4.085179):2.48621):6.990293):5.861938):2.454324):4.035323):4.053834):3.097172):9.010861):3.722819):3.650012):6.62713):5.31985):9.667148):5.638398):107.360427):33.22661):34.657221);
}}

Order phylogeny

;

Polypteriformes : Acipenseriformes : : Lepisosteiformes Amiiformes : : Elopiformes : Anguilliformes : Notacanthiformes Albuliformes : : Osteoglossiformes Hiodontiformes : : Alepocephaliformes : Clupeiformes : Gonorynchiformes : Cypriniformes : Gymnotiformes : Siluriformes Characiformes : Lepidogalaxiiformes : : Argentiniformes : Salmoniformes Esociformes : : Stomiatiformes Osmeriformes : Galaxiiformes : Ateleopodiformes : Aulopiformes : Myctophiformes : : Polymixiiformes : Percopsiformes : Zeiformes : Gadiformes Stylephoriformes : Lampridiformes : : Beryciformes Holocentriformes : Ophidiiformes : Batrachoidiformes : : Labriformes : : Tetraodontiformes Lophiiformes : : Acanthuriformes Ephippiformes : Spariformes : Incertae sedis in Eupercaria : Uranoscopiformes : Perciformes : Centrarchiformes Pempheriformes : : : Gobiiformes Kurtiformes : Syngnathiformes Scombriformes : : : Anabantiformes Synbranchiformes : : Pleuronectiformes Incertae sedis in Carangaria : Carangiformes Istiophoriformes : Mugiliformes : Incertae sedis in Ovalentaria : : Cichliformes Pholidichthyiformes : Atheriniformes : Cyprinodontiformes Beloniformes

Family phylogeny

;

Polypteridae Acipenseridae Polyodontidae Lepisosteidae Amiidae Elopidae Megalopidae Halosauridae Albulidae Synaphobranchidae Anguillidae Serrivomeridae Nemichthyidae Moringuidae Eurypharyngidae Saccopharyngidae Chlopsidae Muraenidae Heterenchelyidae Derichthyidae Colocongridae Congridae Ophichthidae Muraenesocidae Hiodontidae Osteoglossidae Notopteridae Mormyridae Gymnarchidae Alepocephalidae Platytroctidae Denticipitidae Chirocentridae Clupeidae Engraulidae Gonorynchidae Kneriidae Chanidae Cyprinidae Catostomidae Gyrinocheilidae Botiidae Vaillantellidae Cobitidae Ellopostomatidae Nemacheilidae Balitoridae Sternopygidae Hypopomidae Apteronotidae Gymnotidae Rhamphichthyidae Distichodontidae Citharinidae Crenuchidae Lebiasinidae Erythrinidae Ctenoluciidae Chalceidae Characidae Acestrorhynchidae Iguanodectidae Triportheidae Bryconidae Gasteropelecidae Alestidae Parodontidae Chilodontidae Cynodontidae Serrasalmidae Hemiodontidae Anostomidae Curimatidae Prochilodontidae Nematogenyidae Trichomycteridae Callichthyidae Loricariidae Scoloplacidae Diplomystidae Cetopsidae Doradidae Aspredinidae Clariidae Heteropneustidae Siluridae Chacidae Bagridae Horabagridae Schilbeidae Sisoridae Amblycipitidae Akysidae Pangasiidae Plotosidae Pimelodidae Claroteidae Mochokidae Malapteruridae Ariidae Anchariidae Ictaluridae Cranoglanididae Lepidogalaxiidae Salmonidae Esocidae Umbridae Bathylagidae Microstomatidae Argentinidae Opisthoproctidae Retropinnidae Osmeridae Salangidae Plecoglossidae Gonostomatidae Diplophidae Stomiidae Sternoptychidae Phosichthyidae Galaxiidae Ateleopodidae Pseudotrichonotidae Paraulopidae Synodontidae Aulopidae Giganturidae Ipnopidae Bathysauridae Chlorophthalmidae Scopelarchidae Paralepididae Notosudidae Myctophidae Neoscopelidae Polymixiidae Percopsidae Amblyopsidae Aphredoderidae Macrouridae Stylephoridae Zenionidae Parazenidae Zeidae Grammicolepididae Oreosomatidae Cyttidae Veliferidae Lamprididae Lophotidae Trachipteridae Regalecidae Holocentridae Trachichthyidae Melamphaidae Berycidae Stephanoberycidae Rondeletiidae Cetomimidae Barbourisiidae Ophidiidae Bythitidae Batrachoididae Apogonidae Kurtidae Trichonotidae Odontobutidae Rhyacichthyidae Eleotridae Gobiidae Thalasseleotrididae Dactylopteridae Aulostomidae Syngnathidae Centriscidae Pegasidae Fistulariidae Callionymidae Mullidae Champsodontidae Chiasmodontidae Centrolophidae Arripidae Pomatomidae Trichiuridae Gempylidae Scombridae Icosteidae Bramidae Tetragonuridae Stromateidae Nomeidae Ariommatidae Mastacembelidae Chaudhuriidae Synbranchidae Indostomidae Badidae Nandidae Channidae Osphronemidae Anabantidae Helostomatidae Polynemidae Toxotidae Carangidae Leptobramidae Menidae Istiophoridae Xiphiidae Centropomidae Sphyraenidae Lactariidae Psettodidae Citharidae Pleuronectidae Scophthalmidae Achiridae Soleidae Samaridae Rhombosoleidae Bothidae Poecilopsettidae Mugilidae Ambassidae Pseudochromidae Congrogadidae Pomacentridae Embiotocidae Plesiopidae Grammatidae Opistognathidae Gobiesocidae Tripterygiidae Blenniidae Clinidae Chaenopsidae Labrisomidae Polycentridae Cichlidae Pholidichthyidae Atherinopsidae Phallostethidae Atherinidae Melanotaeniidae Bedotiidae Isonidae Adrianichthyidae Exocoetidae Hemiramphidae Belonidae Zenarchopteridae Rivulidae Nothobranchiidae Aplocheilidae Poeciliidae Anablepidae Cyprinodontidae Fundulidae Valenciidae Goodeidae Profundulidae Labridae Pempheridae Glaucosomatidae Lophiidae Ogcocephalidae Antennariidae Chaunacidae Gigantactinidae Ceratiidae Oneirodidae Himantolophidae Melanocetidae Cepolidae Triodontidae Ostraciidae:49 Aracanidae Molidae Tetraodontidae Diodontidae Monacanthidae Balistidae Triacanthidae Triacanthodidae Ephippidae Luvaridae Acanthuridae Zanclidae Siganidae Caproidae Priacanthidae Scatophagidae Sciaenidae Malacanthidae Lethrinidae Sparidae Nemipteridae Hapalogenyidae Lobotidae Chaetodontidae Leiognathidae Pomacanthidae Haemulidae Lutjanidae Monodactylidae Emmelichthyidae Dinopercidae Sillaginidae Moronidae Gerreidae Centrogenyidae Pinguipedidae Uranoscopidae Terapontidae Kuhliidae Kyphosidae Oplegnathidae Enoplosidae Cheilodactylidae Cirrhitidae Percichthyidae Sinipercidae Centrarchidae Elassomatidae Pentacerotidae Banjosidae Lateolabracidae Polyprionidae Acropomatidae Howellidae Dinolestidae Bathyclupeidae Symphysanodontidae Scombropidae Epigonidae Percophidae Creediidae Bembropidae Trachinidae Congiopodidae Percidae Niphonidae Serranidae Platycephalidae Hoplichthyidae Normanichthyidae Sebastidae Scorpaenidae Tetrarogidae Neosebastidae Zanclorhynchidae Triglidae Peristediidae Anoplopomatidae Gasterosteidae Hypoptychidae Aulorhynchidae Zaniolepididae Bathymasteridae Stichaeidae Zoarcidae Cryptacanthodidae Zaproridae Hexagrammidae Trichodontidae Liparidae Cyclopteridae Psychrolutidae Cottidae Jordaniidae Agonidae Scorpaenichthyidae Ereuniidae Rhamphocottidae