diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml new file mode 100644 index 0000000..157b49e --- /dev/null +++ b/.github/workflows/test.yaml @@ -0,0 +1,34 @@ +name: Test + +on: [push, pull_request, workflow_dispatch] + +jobs: + build: + runs-on: ubuntu-latest + + strategy: + matrix: + node-version: [10.x, 12.x, 14.x] + + steps: + - uses: actions/checkout@v2 + - name: Use Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v2 + with: + node-version: ${{ matrix.node-version }} + - name: Cache Node modules + uses: actions/cache@v2 + env: + cache-name: cache-node-modules + with: + # npm cache files are stored in `~/.npm` on Linux/macOS + path: ~/.npm + key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }} + restore-keys: | + ${{ runner.os }}-build-${{ env.cache-name }}- + ${{ runner.os }}-build- + ${{ runner.os }}- + - name: Install dependencies + run: npm install + - name: Test + run: npm test diff --git 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Soc.", + "volume": "2", + "identifier": [] + } + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The crown clade originating in the most recent common ancestor of Cyprinus carpio Linnaeus 1758 (Cypriniformes), Charax (originally Salmo) gibbosus (Linnaeus 1758) (Characiformes), Gymnotus carapo Linnaeus 1758 (Gymnotiformes; Gymnotoidei on the reference phylogeny), Silurus glanis Linnaeus 1758 (Siluriformes; Siluroidei on the reference phylogeny).", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Cyprinus carpio Linnaeus, 1758", + "nameComplete": "Cyprinus carpio" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Charax (originally Salmo) gibbosus Linnaeus, 1758", + "nameComplete": "Charax (originally Salmo) gibbosus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Gymnotus carapo Linnaeus, 1758", + "nameComplete": "Gymnotus carapo" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Silurus glanis Linnaeus, 1758", + "nameComplete": "Silurus glanis" + } + } + ], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000198.json b/phyx/phylonym/CLADO_0000198.json new file mode 100644 index 0000000..0e01843 --- /dev/null +++ b/phyx/phylonym/CLADO_0000198.json @@ -0,0 +1,77 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "Discovery of African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an ancient intercontinental passage.", + "year": 2007, + "authors": [ + { + "name": "J. 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+ } + ], + "phylorefs": [ + { + "regnumId": 198, + "label": "Pan-Siluriformes", + "dwc:scientificNameAuthorship": "Lundberg, J. G.", + "dwc:namePublishedIn": [], + "obo:IAO_0000119": [], + "cladeDefinition": "the total clade of the crown clade Siluriformes.", + "internalSpecifiers": [], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000199.json b/phyx/phylonym/CLADO_0000199.json new file mode 100644 index 0000000..67bcd36 --- /dev/null +++ b/phyx/phylonym/CLADO_0000199.json @@ -0,0 +1,118 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using nuclear rag1 and rag2 gene sequences.", + "year": 2006, + "authors": [ + { + "name": "J. P. Sullivan", + "alternate": [ + "Sullivan, J. P." + ], + "firstname": "J.", + "lastname": "Sullivan", + "middlename": "P." + }, + { + "name": "J. G. Lundberg", + "alternate": [ + "Lundberg, J. 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S.", + "dwc:namePublishedIn": [ + { + "type": "book_section", + "title": "Explorations and surveys for a railroad route from the Mississippi River to the Pacific Ocean.", + "section_title": "Mammals.", + "year": 1857, + "authors": [ + { + "name": "S. F. Baird", + "alternate": [ + "Baird, S. 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Salfeld", + "city": "Berlin", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The smallest crown clade containing Phoca vitulina Linnaeus 1758 (Phocidae), Odobenus rosmarus (Linnaeus 1758), and Otaria byronia (de Blainville 1820) (Otariidae).", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Phoca vitulina Linnaeus, 1758", + "nameComplete": "Phoca vitulina" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Odobenus rosmarus Linnaeus, 1758", + "nameComplete": "Odobenus rosmarus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Otaria byronia de Blainville, 1820", + "nameComplete": "Otaria byronia" + } + } + ], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000273.json b/phyx/phylonym/CLADO_0000273.json new file mode 100644 index 0000000..d28cd63 --- /dev/null +++ b/phyx/phylonym/CLADO_0000273.json @@ -0,0 +1,109 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "A toothed turtle from the Late Jurassic of China and the global biogeographic history of turtles.", + "year": 2016, + "authors": [ + { + "name": "W. 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Xu", + "alternate": [ + "Xu, X." + ], + "firstname": "X.", + "lastname": "Xu" + } + ], + "editors": [], + "series_editors": [], + "figure": "8", + "identifier": [ + { + "type": "doi", + "id": "10.1186/s12862-016-0762-5" + } + ], + "link": [], + "journal": { + "name": "BMC Evolutionary Biology", + "volume": "16", + "identifier": [] + } + }, + "newick": "(Sphenodon_punctatus, \n(Anthodon_serrarius, Owenetta_kitchingorum,\n(Odontochelys_Semitestacea, (Proganochelys_quenstedti, \n((Australochelys_africanus, Paleochersis_talampayensis),\n(Proterochersis_robusta, \n((Chondorchelys_antiqua, Kayentachelys_aprix), \n((Spoochelys_ormondea, Chubutemys_copelloi, \n(Peligrochelys, (Niolamia_argentina, (Ninjemys_oweni, \n(Meiolania_platyceps, Warkalania_carinaminor))))),\n((Sichuanchelys_chowi, Sichuanchelys_palatodentata, Mongolochelys_efremovi),\n((Otwayesmys_cunicularius, (Naomichelys_speciosa, Helochelydra_nopcsai)),\n(Kallokibotion_bajazidi, \n((Dorsetochelys_delairi, ((Glyptops_plicatulus, Pleurosternon_bullockii), \n(Neurankylus_eximius, (Trinitichelys_hiatii, (Plesiobaena_antiqua, \n(Chisternon_undatum, Baena_arenosa, Boremys_pulchra)))))),\n\n((\n(Notoemys_laticentralis, (Caribemys_oxfordiensios, Platychelys_oberndorferi)), \n((Araripemys_barretoi, (Pelomedusa_subrufa, \n(Podocnemis_expansa, Erymonochelys_madagascariensis))),\n(Yaminuechelys_maior, Prochelidella_cerrobarcinae, \n((Chelus_fimbriatus, Phrynops_geoffroanus), \n((Chelodina_longicollis, Chelodina_colliei), (Myuchelys_latisternum, \nElseya_dentata)))))),\n\n\n(Thalassemys_moseri, \n(Plesiochelys_etalloni, Portlandemyus_macdowelli, \n(Solnhofia_parsonsi, \n\n(((Siamochelys_peninsularis, (Annemys_levensis, \n(Xinjiangchelys_radiplicatoides, Annemys_latiens, Xinjiangchelys_wusu))),\n((Changmachelys_bohlini, (Judithemys_sukhanovi, Hangaiemys_hoburensis)),\n(Xiaochelys_ningchengensis, ((Liaochelys_jianchangensis, Ordosemys_leios),\n(Manchurochelys_manchoukuoensis, (Dracochelys_bicuspis, \n(Sinemys_gamera, Sinemys_lens, Sinemys_brevispinus))))))),\n\n((Shachemys_laosiana, \n(((Basilochelys_macrobios_Yehguia_tatsuensis), \n(Adocus_beatus, Basilemys_variolosa)), \n(Carettochelys_insculpta, Anosteria_ornata, \n(Lissemys_punctata, Plastomenus_aff_thomassii, \n(Pelodiscus_sinensis, Apalone_spinifera))))), \n\n(((Platysternon_megacephalum, (Emys_orbicularis, (Mongolemys_elegans, \n(Trachemys_scripta, Chrysemys_picta)))), \n(Echmatemys_wyomingensis, (Geoclemys_hamiltonii, (Stylemys_nebraskensis, \n(Gopherus_polyphemus, (Eurotestudo_hermanni, \n(Chelonoidis_chilensis, Chelnoidis_gringorum))))))),\n\n((Toxochelys_latiremys, \n((Dermochelys_coriacea, Mesodermochelys_undulatus), \n(Chelonia_mydas, Caretta_caretta))), \n\n((Protochelydra_zangerli, (Chelydra_serpentina, \nMacroclemys_temminckii, Macroclemys_schmidti)), \n(Emarginachelys_cretacea, \n((Hoplochelys_crassa, \n(Dermatemys_mawii, Baptemys_wyomingensis)), \n(Staurotypus_triporcatus, Xenochelys_formosa, \n(Kino_sternon_flavescens, Sternotherus_odoratus)))))))))))))))))))))))))" + } + ], + "phylorefs": [ + { + "regnumId": 273, + "label": "Testudinata", + "dwc:scientificNameAuthorship": "Joyce, W. G., Parham, J. F., Anquetin, J., Claude, J., Danilov, I. G., Iverson, J. B., Kear, B., Lyson, T. R., Rabi, M., Sterli, J.", + "dwc:namePublishedIn": [ + { + "type": "book", + "title": "Klassification und kurze Geschichte der Vierfüßigen Thiere (translation by F. D. Behn).", + "year": 1760, + "authors": [ + { + "name": "I. T. Klein", + "alternate": [ + "Klein, I. T." + ], + "firstname": "I.", + "lastname": "Klein", + "middlename": "T." + } + ], + "editors": [], + "series_editors": [], + "publisher": "Jonas Schmidt", + "city": "Lübeck", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The apomorphy-based clade name, for which a complete turtle shell, as inherited by Testudo graeca Linnaeus 1758 is an apomorphy. A 'complete turtle shell' is herein defined as a composite structure consisting of a carapace with interlocking costals, neurals, peripherals, and a nuchal, together with the plastron comprising interlocking epi-, hyo-, meso- (lost in Testudo graeca), hypo-, xiphiplastra and an entoplastron.", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000109", + "label": "Testudo graeca Linnaeus, 1758", + "nameComplete": "Testudo graeca" + } + } + ], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000274.json b/phyx/phylonym/CLADO_0000274.json new file mode 100644 index 0000000..39db4d6 --- /dev/null +++ b/phyx/phylonym/CLADO_0000274.json @@ -0,0 +1,136 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles.", + "year": 2017, + "authors": [ + { + "name": "A. G. Pereira", + "alternate": [ + "Pereira, A. G." + ], + "firstname": "A.", + "lastname": "Pereira", + "middlename": "G." + }, + { + "name": "J. Sterli", + "alternate": [ + "Sterli, J." + ], + "firstname": "J.", + "lastname": "Sterli" + }, + { + "name": "F. R. R. Moreira", + "alternate": [ + "Moreira, F. R. R." + ], + "firstname": "F. R.", + "lastname": "Moreira", + "middlename": "R." + }, + { + "name": "C. G. Schrago", + "alternate": [ + "Schrago, C. G." + ], + "firstname": "C.", + "lastname": "Schrago", + "middlename": "G." + } + ], + "editors": [], + "series_editors": [], + "figure": "1", + "identifier": [ + { + "type": "doi", + "id": "10.1016/j.ympev.2017.05.008" + } + ], + "link": [], + "journal": { + "name": "Molecular Phylogenetics and Evolution", + "volume": "113", + "identifier": [] + } + } + } + ], + "phylorefs": [ + { + "regnumId": 274, + "label": "Testudines", + "dwc:scientificNameAuthorship": "Joyce, W. G., Parham, J. F., Anquetin, J., Claude, J., Danilov, I. G., Iverson, J. B., Kear, B., Lyson, T. R., Rabi, M., Sterli, J.", + "dwc:namePublishedIn": [ + { + "type": "book", + "title": "Versuch einer Anleitung, zur Kenntniß und Geschichte der Thiere und Mineralien.", + "year": 1788, + "authors": [ + { + "name": "A. J. G. C. Batsch", + "alternate": [ + "Batsch, A. J. G. C." + ], + "firstname": "A.", + "lastname": "Batsch", + "middlename": "J. G. C." + } + ], + "editors": [], + "series_editors": [], + "publisher": "Akademische Buchhandlung", + "city": "Jena", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The smallest crown clade containing the pleurodire Chelus (originally Testudo) fimbriatus Schneider 1783, the trionychian Trionyx (originally Testudo) triunguis Forskål 1775, the americhelydian Chelonia (originally Testudo) mydas Linnaeus 1758, and the testudinoid Testudo graeca Linnaeus 1758.", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Chelus (originally Testudo) fimbriatus Schneider, 1783", + "nameComplete": "Chelus (originally Testudo) fimbriatus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Trionyx (originally Testudo) triunguis Forskål, 1775", + "nameComplete": "Trionyx (originally Testudo) triunguis" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Chelonia (originally Testudo) mydas Linnaeus, 1758", + "nameComplete": "Chelonia (originally Testudo) mydas" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Testudo graeca Linnaeus, 1758", + "nameComplete": "Testudo graeca" + } + } + ], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000275.json b/phyx/phylonym/CLADO_0000275.json new file mode 100644 index 0000000..0eeb025 --- /dev/null +++ b/phyx/phylonym/CLADO_0000275.json @@ -0,0 +1,121 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "A toothed turtle from the Late Jurassic of China and the global biogeographic history of turtles.", + "year": 2016, + "authors": [ + { + "name": "W. G. Joyce", + "alternate": [ + "Joyce, W. G." + ], + "firstname": "W.", + "lastname": "Joyce", + "middlename": "G." + }, + { + "name": "M. Rabi", + "alternate": [ + "Rabi, M." + ], + "firstname": "M.", + "lastname": "Rabi" + }, + { + "name": "J. M. Clark", + "alternate": [ + "Clark, J. M." + ], + "firstname": "J.", + "lastname": "Clark", + "middlename": "M." + }, + { + "name": "X. Xu", + "alternate": [ + "Xu, X." + ], + "firstname": "X.", + "lastname": "Xu" + } + ], + "editors": [], + "series_editors": [], + "figure": "8", + "identifier": [ + { + "type": "doi", + "id": "10.1186/s12862-016-0762-5" + } + ], + "link": [], + "journal": { + "name": "BMC Evolutionary Biology", + "volume": "16", + "identifier": [] + } + } + } + ], + "phylorefs": [ + { + "regnumId": 275, + "label": "Pan-Pleurodira", + "dwc:scientificNameAuthorship": "Joyce, W. G., Parham, J. F., Anquetin, J., Claude, J., Danilov, I. G., Iverson, J. B., Kear, B., Lyson, T. R., Rabi, M., Sterli, J.", + "dwc:namePublishedIn": [ + { + "type": "book", + "title": "Developing a protocol for the conversion of rank-based taxon names to phylogenetically defined clade names, as exemplified by turtles.", + "year": 2004, + "authors": [ + { + "name": "W. G. Joyce", + "alternate": [ + "Joyce, W. G." + ], + "firstname": "W.", + "lastname": "Joyce", + "middlename": "G." + }, + { + "name": "J. F. Parham", + "alternate": [ + "Parham, J. F." + ], + "firstname": "J.", + "lastname": "Parham", + "middlename": "F." + }, + { + "name": "J. A. Gauthier", + "alternate": [ + "Gauthier, J. A." + ], + "firstname": "J.", + "lastname": "Gauthier", + "middlename": "A." + } + ], + "editors": [], + "series_editors": [], + "publisher": "Journal of Paleontology", + "pages": "989-1013", + "identifier": [ + { + "type": "doi", + "id": " DOI: https://doi.org/10.1666/0022-3360(2004)078<0989:DAPFTC>2.0.CO;2" + } + ], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The total clade of crown clade Pleurodira.", + "internalSpecifiers": [], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000276.json b/phyx/phylonym/CLADO_0000276.json new file mode 100644 index 0000000..98fb34c --- /dev/null +++ b/phyx/phylonym/CLADO_0000276.json @@ -0,0 +1,132 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "Multilocus phylogeny and statistical biogeography clarify the evolutionary history of major lineages of turtles.", + "year": 2017, + "authors": [ + { + "name": "A. G. Pereira", + "alternate": [ + "Pereira, A. G." + ], + "firstname": "A.", + "lastname": "Pereira", + "middlename": "G." + }, + { + "name": "J. Sterli", + "alternate": [ + "Sterli, J." + ], + "firstname": "J.", + "lastname": "Sterli" + }, + { + "name": "F. R. R. Moreira", + "alternate": [ + "Moreira, F. R. R." + ], + "firstname": "F. R.", + "lastname": "Moreira", + "middlename": "R." + }, + { + "name": "C. G. Schrago", + "alternate": [ + "Schrago, C. 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G., Parham, J. F., Anquetin, J., Claude, J., Danilov, I. G., Iverson, J. B., Kear, B., Lyson, T. R., Rabi, M., Sterli, J.", + "dwc:namePublishedIn": [ + { + "type": "article", + "title": "Third contribution to the herpetology of tropical America.", + "year": 1865, + "authors": [ + { + "name": "E. D. Cope", + "alternate": [ + "Cope, E. 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Part II.", + "year": 1874, + "authors": [ + { + "name": "A. H. Garrod", + "alternate": [ + "Garrod, A. H." + ], + "firstname": "A.", + "lastname": "Garrod", + "middlename": "H." + } + ], + "editors": [], + "series_editors": [], + "publisher": "Proc. Zool. Soc.", + "city": "London", + "pages": "111-123", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The smallest crown clade containing Charadrius hiaticula Linnaeus 1758 (Charadrii), Scolopax minor J. F. Gmelin 1789 (Scolopaci) and Larus marinus Linnaeus 1758 (Lari).", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Charadrius hiaticula Linnaeus, 1758", + "nameComplete": "Charadrius hiaticula" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Scolopax minor Gmelin, 1789", + "nameComplete": "Scolopax minor" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Larus marinus Linnaeus, 1758", + "nameComplete": "Larus marinus" + } + } + ], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/CLADO_0000283.json b/phyx/phylonym/CLADO_0000283.json new file mode 100644 index 0000000..78f21c1 --- /dev/null +++ b/phyx/phylonym/CLADO_0000283.json @@ -0,0 +1,209 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "Seabird supertrees: combining partial estimates of procellariiform phylogeny.", + "year": 2002, + "authors": [ + { + "name": "M. 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oplasmatales_Entomoplasmataceae_Entomoplasma_luminosum_ATCC_49195:0.1715805):0.06926308[94],Bacteria_Tenericutes_Mollicutes_Entomoplasmatales_Spiroplasmataceae_Spiroplasma_culicicola_AES_1:0.1350548):0.22531392[100],((Bacteria_Tenericutes_Mollicutes_Mycoplasmatales_Mycoplasmataceae_Mycoplasma_agalactiae:0.5187169,Bacteria_Tenericutes_Mollicutes_Mycoplasmatales_Mycoplasmataceae_Candidatus_Hepatoplasma_crinochetorum_Av:0.47773317):0.07354273[78],Bacteria_Tenericutes_Mollicutes_Mycoplasmatales_Mycoplasmataceae_Ureaplasma_parvum_serovar_3_str._ATCC_27815:0.6445851):0.1251894[100]):0.117267735[100]):0.09259834[100],((((Bacteria_Tenericutes_Mollicutes_Mollicutes_bacterium_HR1:0.13826124,Bacteria_Tenericutes_Mollicutes_Mollicutes_bacterium_HR2:0.13241401):0.12579179[100],(Bacteria_Tenericutes_Mollicutes_Acholeplasmatales_Acholeplasmataceae_Candidatus_Phytoplasma_aster_yellows_witches_broom_AY_WB:0.35381117,Bacteria_Tenericutes_Mollicutes_Acholeplasmatales_Acholeplasmataceae_Acholeplasma_laidlawii_PG_8A:0.20988363):0.17748766[100]):0.071037404[99],Bacteria_unclassified_Bacteria_Haloplasmatales_Haloplasmataceae_Haloplasma_contractile_SSD_17B:0.18698274):0.035505217[79],Bacteria_Firmicutes_Erysipelotrichi_Erysipelotrichales_Erysipelotrichaceae_Turicibacter_sp._HGF1_contig00015:0.17516553):0.034631588[74]):0.087114014[100]):0.015948912[27],((Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Anoxybacillus_flavithermus_WK1:0.042964816,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Geobacillus_kaustophilus_HTA426:0.056369092):0.047190864[100],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Geobacillus_debilis_gb1_GenePRIMP:0.1076793):0.034448083[96]):0.028242633[62],(((((((((Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Salimicrobium_sp._MJ3:0.13940398,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Halobacillus_halophilus_DSM_2266:0.051227804):0.04561813[100],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Thalassobacillus_devorans_MSP14:0.061416406):0.022728167[81],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Pontibacillus_halophilus_DSM_19796:0.12652065):0.025492413[68],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Terribacillus_aidingensis_MP602:0.11443007):0.0140317585[21],(Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Gracilibacillus_lacisalsi_DSM_19029:0.09086943,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Sediminibacillus_halophilus_NSP9.3:0.04843369):0.023528272[62]):0.016560854[17],(((Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Paucisalibacillus_globulus_DSM_18846:0.034673892,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Ornithinibacillus_sp._TW25:0.026289757):0.05823782[100],(Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Virgibacillus_sp._CM_4:0.051554494,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Oceanobacillus_iheyensis_HTE831:0.074836105):0.018253477[49]):0.0144994985[52],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Lentibacillus_sp._Grbi:0.095756084):0.031381186[100]):0.01983699[40],((Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Halalkalibacillus_halophilus_DSM_18494:0.07657252,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Alkalibacillus_haloalkaliphilus_C5:0.08818368):0.08477452[100],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Amphibacillus_xylanus_NBRC_15112:0.13542163):0.022354595[44]):0.06080992[100],((Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Salsuginibacillus_kocurii_DSM_18087:0.14161316,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Marinococcus_halotolerans_DSM_16375:0.14169781):0.07046356[100],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Bacillus_selenitireducens_MLS10:0.14033839):0.037768807[99]):0.0341527[89],((Bacteria_Firmicutes_Bacilli_Bacillales_Sporolactobacillaceae_Sporolactobacillus_terrae_HKM_1:0.17238638,Bacteria_Firmicutes_Bacilli_Bacillales_Sporolactobacillaceae_Tuberibacillus_calidus_DSM_17572:0.09854769):0.058277983[100],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Bacillus_gelatini_DSM_15865:0.10136248):0.025571149[83]):0.016422655[18]):0.024969049[29],Bacteria_Firmicutes_Bacilli_Bacillales_Bacillales_incertae_sedis_Bacillales_Family_XII._Incertae_Sedis_Exiguobacterium_sp._AT1b:0.20245627):0.0758301[100],(Bacteria_Firmicutes_Bacilli_Bacillales_Bacillaceae_Caldalkalibacillus_thermarum_TA2.A1_ctg240:0.098820716,Bacteria_Firmicutes_Bacilli_Bacillales_Bacillales_incertae_sedis_Bacillales_Family_X._Incertae_Sedis_Thermicanus_aegyptius_DSM_12793:0.20486817):0.036274534[56]):0.02028692[65],(Bacteria_Firmicutes_Bacilli_Bacillales_Paenibacillaceae_Aneurinibacillus_group_Aneurinibacillus_terranovensis_DSM_18919:0.12247822,Bacteria_Firmicutes_Bacilli_Bacillales_Paenibacillaceae_Brevibacillus_brevis_NBRC_100599:0.14864206):0.053873707[99]):0.023728278[73],(((Bacteria_Firmicutes_Bacilli_Bacillales_Paenibacillaceae_Saccharibacillus_sacchari_GR21_DSM_19268:0.10283499,Bacteria_Firmicutes_Bacilli_Bacillales_Paenibacillaceae_Paenibacillus_lactis_154:0.052747056):0.035401203[100],Bacter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"(Latimeria_chalumnae_1114,(((Didelphis_marsupialis_1092\n,Gazella_thomsoni_1093),((Alligator_sinensis_1090,Iguana_iguana_1001)\n,(Chelydra_serpentina_1091,Pelomedusa_subrufa_1051))),(((Epicrionops_sp_917\n,Rhinatrema_bivittatum_TJ29),((Ichthyophis_sp_TJ102\n,(Ichthyophis_peninsularis_878,Uraeotyphlus_narayani_882))\n,((Boulengerula_uluguruensis_879,Herpele_squalostoma_TJ122)\n,((Caecilia_tentaculata_TJ52,Typhlonectes_natans_877)\n,((Crotaphatrema_tchabalmbaboensis_TJ118,Scolecomorphus_vittatus_TJ104)\n,((Geotrypetes_seraphini_TJ103,(Dermophis_oaxacae_TJ99\n,Schistometopum_gregorii_881)),(Gegeneophis_ramaswamii\n,(Hypogeophis_rostratus_918,Siphonops_hardyi_880))))))))\n,((((Batrachuperus_pinchoni_TJ105,Ranodon_sibiricus)\n,(Cryptobranchus_alleganiensis_1050,(Andrias_davidianus\n,Andrias_japonicus_1059))),((((Necturus_alabamensis_938\n,Necturus_maculosus_TJ6),(Pseudobranchus_striatus_969,(Siren_intermedia\n,Siren_lacertina_968))),(((Dicamptodon_aterrimus_909\n,Dicamptodon_tenebrosus_1048),(Ambystoma_cingulatum_970\n,(Ambystoma_mexicanum_996,Ambystoma_tigrinum_TJ53)))\n,(Salamandra_salamandra_TJ88,((Pleurodeles_waltl_TJ91\n,Tylototriton_shanjing_TJ4),((Notophthalmus_viridiscens_TJ7,Taricha_sp_TJ90)\n,((Pachytriton_brevipes_TJ92,Paramesotriton_sp_TJ76),(Neurergus_crocatus\n,(Euproctus_asper,Triturus_sp_TJ89)))))))),(Rhyacotriton_cascadae_900\n,(Amphiuma_tridactylum_910,((Plethodon_dunni_1049,((Ensatina_eschscholtzii\n,Plethodon_jordani_915),(Aneides_hardii,((Desmognathus_quadramaculatus_1040\n,Desmognathus_wrighti),(Phaeognathus_hubrichti\n,(Hydromantes_platycephalus_1013,Speleomantes_italicus))))))\n,((Batrachoseps_attenuatus,Batrachoseps_wrightorum)\n,(Hemidactylum_scutatum_911,((Eurycea_wilderae_1041\n,Gyrinophilus_porphyriticus_1042),((Nototriton_abscondens,(Oedipina_uniformis\n,(Cryptotriton_alvarezdeltoroi,Dendrotriton_rabbi))),(Thorius_sp_TJ100\n,((Bolitoglossa_rufescens_TJ101,Parvimolge_townsendi),(Ixalotriton_niger\n,(Lineatriton_lineolus,Pseudoeurycea_conanti_TJ98)))))))))))))\n,((Ascaphus_truei_907,(Leiopelma_archeyi_998,Leiopelma_hochstetteri_999))\n,((Rhinophrynus_dorsalis_899,(Hymenochirus_boettgeri,((Pipa_carvalhoi_1038\n,Pipa_pipa_457),(Silurana_tropicalis_TJ128,(Xenopus_gilli_TJ9,Xenopus_laevis)\n)))),(((Alytes_obstetricans_902,(Discoglossus_galganoi_1029\n,Discoglossus_pictus_TJ83)),(Bombina_microdeladigitora_TJ54\n,(Bombina_orientalis_TJ80,(Bombina_bombina_1035,Bombina_variegata_1034))))\n,(((Pelodytes_puntatus_901,(Spea_hammondii_966,(Scaphiopus_couchii_937\n,Scaphiopus_holbrooki_943))),((Pelobates_cultripes,Pelobates_fuscus_903)\n,((Leptolalax_pelodytoides_TJ25,(Leptobrachium_chapaense_450\n,Leptobrachium_hasselti_1022)),((Megophrys_nasuta_TJ107\n,(Ophryophryne_microstoma_TJ36,Ophryophryne_poilani_TJ21))\n,(Brachytarsophrys_feae,(Xenophrys_major,Xenophrys_major_TJ19))))))\n,((Heleophryne_purcelli_633,Heleophryne_regis_906)\n,((((Kalophrynus_pleurostigma_933,(Synapturanus_mirandaribeiroi_530\n,((Micryletta_inornata,Phrynomantis_bifasciatus_941)\n,((((Hoplophryne_rogersi_TJ68,Ramanella_obscura),((Anodonthyla_montana\n,Platypelis_sp_TJ58),(Plethodontohyla_sp_TJ56,Stumpffia_sp_TJ59)))\n,((Ctenophryne_geayei_TJ27,Nelsonophryne_aequatorialis)\n,(Dasypops_schirchi_888,(Hamptophryne_boliviana_TJ86\n,(Elachistocleis_ovalis_TJ51,(Dermatonotus_muelleri_1185\n,(Gastrophryne_elegans_TJ74,Gastrophryne_olivacea_1053)))))))\n,((Scaphiophryne_marmorata_TJ57,(Kaloula_pulchra_TJ41,(Chaperina_fusca_932\n,(Calluella_guttulata_931,(Microhyla_heymonsi_TJ26,Microhyla_sp_TJ70)))))\n,(Dyscophus_guineti_TJ82,((Choerophryne_sp_991,Cophixalus_sphagnicola_990)\n,((Genyophryne_thomsoni_993,(Copiula_sp_992,Sphenophryne_sp_989))\n,(Liophryne_rhododactyla_983,(Aphantophryne_pansa_980,(Callulops_slateri\n,Oreophryne_brachypus_979))))))))))),((Hemisus_marmoratus_TJ78\n,(Breviceps_mossambicus_942,(Probreviceps_macrodactylus_TJ69\n,(Callulina_kisiwamsitu_TJ77,Callulina_kreffti)))),(((Acanthixalus_spinosus\n,(Kassina_senegalensis_TJ85,Phlyctimantis_leonardi_TJ119))\n,(Opisthothylax_immaculatus_962,(((Afrixalus_fornasinii_TJ44\n,Afrixalus_pygmaeus_1019),(Tachycnemis_seychellensis_TJ95\n,(Heterixalus_sp_TJ93,Heterixalus_tricolor))),(Cryptothylax_gresshoffi_959\n,((Alexteroon_obstetricans_960,Alexteroon_obstetricans_TJ109)\n,(Hyperolius_tuberilinguis_TJ43,(Hyperolius_alticola_1011\n,(Hyperolius_punticulatus_TJ35,Nesionixalus_thomensis_1017))))))))\n,((Leptopelis_argenteus_1012,(Leptopelis_bocagei_TJ67,(Leptopelis_sp_950\n,Leptopelis_vermiculatus_1026))),((Leptodactylodon_bicolor_TJ129\n,(Nyctibates_corrugatus_TJ126,(Astylosternus_schiotzi_TJ116\n,Trichobatrachus_robustus_TJ111))),(Scotobleps_gabonicus_TJ130\n,((Cardioglossa_gratiosa_964,Cardioglossa_leucomystax_845)\n,((Schoutedenella_sylvatica_844,Schoutedenella_taeniata_1018)\n,((Arthroleptis_tanneri_TJ75,Arthroleptis_variabilis_847)\n,(Schoutedenella_schubotzi_1021,Schoutedenella_xenodactyloides_TJ79))))))))))\n,((Ptychadena_mascareniensis_181,(Ptychadena_anchietae\n,Ptychadena_cooperi_588)),((Ingerana_baluensis_929,(Discodeles_guppyi_984\n,(Ceratobatrachus_guentheri_982,(Batrachylodes_vertebralis_994\n,(Platymantis_pelewensis_896,Platymantis_weberi_981))))),((Micrixalus_fuscus\n,Micrixalus_kottigeharensis),((((Phrynobatrachus_dendrobates_1015\n,Phrynodon_sandersoni_848),((Dimorphognathus_africanus_963\n,(Phrynobatrachus_auritus_849,Phrynobatrachus_natalensis_TJ61))\n,(Phrynobatrachus_calcaratus_1024,(Phrynobatrachus_dispar_1009\n,Phrynobatrachus_mababiensis_TJ72)))),(((Conraua_goliath_919\n,Conraua_robusta_TJ113),((Indirana_sp1_FB2000a,Indirana_sp2_FB2000b)\n,(Arthroleptides_sp_TJ62,(Petropedetes_palmipes_841,(Petropedetes_newtoni_965\n,(Petropedetes_cameronensis_843,Petropedetes_parkeri))))))\n,((Pyxicephalus_edulis_944,(Aubria_subsigillata_961\n,Aubria_subsigillata_TJ117)),(Tomopterna_delalandii_TJ5\n,((Arthroleptella_bicolor_591,Natalobatrachus_bonebergi)\n,((Afrana_fuscigula_590,(Afrana_angolensis_1014,Amietia_vertebralis_TJ45))\n,(Strongylopus_grayii_589,(Anhydrophryne_rattrayi,Cacosternum_platys_1045))))\n)))),(((Micrixalus_borealis_1020,(Occidozyga_baluensis_930\n,(Occidozyga_laevis_TJ12,Occidozyga_lima_1010))),((Limnonectes_kuhlii_TJ14\n,(Limnonectes_grunniens_986,(Limnonectes_blythi_TJ22,(Taylorana_limborgi\n,(Limnonectes_acanthi,(Limnonectes_heinrichi,Limnonectes_visayanus))))))\n,((Paa_verrucospinosa_TJ23,Quasipaa_exilispinosa_1030),(Nanorana_pleskei\n,((Fejervarya_cancrivorus,Fejervarya_limnocharis_TJ15)\n,((Sphaerotheca_breviceps_893,Sphaerotheca_pluvialis)\n,((Fejervarya_kirtisinghei,Fejervarya_syhadrensis),(Nannophrys_ceylonensis\n,(Euphlyctis_cyanophlyctis,(Hoplobatrachus_occipitalis_513\n,Hoplobatrachus_rugulosus_928)))))))))),((((Boophis_albilabris_185\n,Boophis_tephraeomystax_182),((Aglyptodactylus_madagascariensis_505\n,Laliostoma_labrosum_508),((Mantella_aurantiaca_238,Mantella_nigricans_204)\n,(Mantidactylus_cf_femoralis_187,Mantidactylus_peraccae_272))))\n,(Buergeria_japonica_502,(Philautus_gracilipes_446\n,((Chirixalus_eiffingeri_912,Chirixalus_idiooticus_500),(((Nyctixalus_905\n,Nyctixalus_pictus_920),(Philautus_rhododiscus_TJ37,Theloderma_corticale_445)\n),((Rhacophorus_annamensis_441,(Rhacophorus_bipunctatus_440\n,(Rhacophorus_calcaneus_TJ24,Rhacophorus_orlovi_443))),((Polypedates_cruciger\n,Polypedates_leucomystax_442),(Chirixalus_vittatus_921,(Chirixalus_doriae_922\n,Chiromantis_xerampelina_TJ42))))))))),((Lankanectes_corrugatus\n,(Nyctibatrachus_cf_aliciae,Nyctibatrachus_major)),(Staurois_tuberlinguis_927\n,((Sylvirana_guentheri_1052,(Hylarana_erythraea_925\n,Hylarana_taipehensis_TJ40)),(((Chalcorana_chalconota_926\n,(Amnirana_albilabris_TJ131,Amnirana_galamensis_512))\n,((Sylvirana_maosonensis_TJ18,Sylvirana_nigrovittata_TJ16)\n,(Sylvirana_temporalis,(Papurana_daemeli_985,Tylerana_arfaki_987))))\n,((Clinotarsus_curtipes,Meristogenys_orphnocnemis_934),(Glandirana_minima\n,((Amolops_hongkongensis,(Pelophylax_nigromaculata_924,Pelophylax_ridibunda))\n,(((Nidirana_adenopleura_908,Nidirana_chapaensis_TJ13)\n,((Amolops_chapaensis_TJ17,Odorrana_grahami_1025),(Huia_nasica_TJ11\n,Odorrana_livida_TJ38))),(((Amerana_mucosa_976,Aurorana_aurora_975)\n,(Pseudorana_johnsi_997,(Rana_japonica_923,(Pseudoamalops_sauteri_914\n,Rana_temporaria_916)))),((Aquarana_grylio_972,(Aquarana_heckscheri_977\n,(Aquarana_catesbeiana_1044,Aquarana_clamitans_971))),(Rana_sylvatica_TJ33\n,((Lithobates_palmipes_TJ28,(Sierrana_maculata_1076\n,Trypheropsis_warszewitschii_1043)),(Pantherana_capito_973\n,((Pantherana_chiricahuensis_1055,Pantherana_pipiens_913)\n,(Pantherana_berlandieri,(Pantherana_forreri_895\n,Pantherana_yavapaiensis_1057))))))))))))))))))))))),(((Nasikabatrachidae_sp\n,Nasikabatrachus_sahyadrensis),(Nesomantis_thomasseti_TJ96\n,Sooglossus_sechellensis_TJ94)),(((Caudiverbera_caudiverbera_TJ87\n,Telmatobufo_venustus_1131),((Kyarranus_sphagnicolus_1084\n,(Adelotus_brevis_1073,(((Neobatrachus_pictus_1070,Neobatrachus_sudelli_673)\n,(Notaden_melanoscaphus_1068,(Lechriodus_fletcheri_1065\n,Limnodynastes_ornatus_1064))),(Heleioporus_australiacus_1079\n,(Limnodynastes_dumerilli_1067,((Limnodynastes_depressus_1080\n,Limnodynastes_peronii_1032),(Limnodynastes_salmini\n,Megistolotis_lignarius_1069))))))),((Mixophyes_carbinensis_1086\n,Rheobatrachus_silus_1061),(Taudactylus_acutirostris_1062\n,(((Bryobatrachus_nimbus_1074,Crinia_signifera_978),(Paracrinia_haswelli_1077\n,(Assa_darlingtoni_1066,Geocrinia_victoriana_1072)))\n,((Spicospina_flammocaerulea_1075,Uperoleia_laevigata_1003)\n,((Pseudophryne_bibroni_677,Pseudophryne_coriacea_1082)\n,(Myobatachus_gouldii_1081,(Arenophryne_sp_1155,Metacrinia_nichollsi_1071))))\n))))),(Hemiphractus_helioi_467,((((Eleutherodactylus_binotatus_884\n,Ischnocnema_sp_521),(Barycholos_ternetzi_887,(Brachycephalus_ephippium_883\n,Eleutherodactylus_juipoca_886))),((Craugastor_pluvicanorus_TJ31\n,(Euhyas_planirostris_898,(Syrrhophus_marnockii_894,Syrrhophus_nitidus_1087))\n),((Phrynopus_sp_KU_202652,Phrynopus_sp_TJ30),(Craugastor_bufoniformis_954\n,((Craugastor_alfredi_1089,Craugastor_augusti_1056),(Craugastor_rhodopis_1088\n,(Craugastor_punctariolus_957,Craugastor_ranoides_897)))))))\n,((Cryptobatrachus_sp,Stefania_evansi_417),((Flectonotus_sp_690\n,(Gastrotheca_cf_marsupiata_317,Gastrotheca_fissipes_825))\n,(((((Agalychnis_calcarifer_1006,Phyllomedusa_vaillanti_103)\n,(Agalychnis_callidryas_TJ71,Phasmahyla_guttata_687)),((Litoria_meiriana_675\n,(Litoria_freycineti_672,Litoria_inermis_995)),(Nyctimistes_pulchra_676\n,((Litoria_nannotis_1000,Nyctimystes_dayi_1002),((Cyclorana_australis_674\n,Litoria_aurea_543),(Litoria_genimaculata_1004,Litoria_lesueurii_988))))))\n,(((Sphaenorhynchus_lacteus_138,(Scinax_garbei_90,Scinax_ruber_16))\n,((Hyloscirtus_armata_318,Hyloscirtus_palmeri_504),(Hypsiboas_granosus_416\n,((Aplastodiscus_perviridis_4,Hypsiboas_albomarginata_140)\n,(Hypsiboas_boans_486,Hypsiboas_multifasciata_102)))))\n,(((Scarthyla_goinorum_86,(Lysapsus_laevis_629,Pseudis_paradoxa_704))\n,(Dendropsophus_minutus_35,(Dendropsophus_marmoratus_468\n,(Dendropsophus_nana_172,Dendropsophus_parviceps_80))))\n,((Phyllodytes_luteolus_823,((Osteocephalus_cf_taurinus_410\n,Osteopilus_septentrionalis_139),(Argenteohyla_siemersi_pederseni_292\n,(Trachycephalus_jordani_540,Trachycephalus_venulosus_94))))\n,((Ecnomiohyla_miliaria_639,(Duellmanohyla_rufioculis_211\n,Ptychohyla_leonhardschultzei_796)),(Charadrahyla_nephila_551\n,(((Exerodonta_chimalapa_549,Plectrohyla_guatemalensis_802)\n,(Acris_crepitans_604,(Pseudacris_crucifer_638,Pseudacris_triseriata_833)))\n,((Hyla_arborea_871,Isthmohyla_rivularis_210),((Hyla_cinerea_207\n,Tlalocohyla_picta_658),(Smilisca_phaeota_459,(Anotheca_spinosa_552\n,Triprion_petasatus_458))))))))))),(((Allophryne_ruthveni_837\n,(Hyalinobatrachium_fleischmanni_TJ97,(Centrolene_prosoblepon_827\n,(Centrolene_geckoideum,Cochranella_bejaranoi_311))))\n,((Pleurodema_brachyops_630,(Edalorhina_perezi_531,Physalaemus_cuvieri_TJ65))\n,(Pseudopaludicola_sp_650,((Paratelmatobius_sp_891,Scythrophrys_sawayae_892)\n,((Adenomera_hylaedactyla_529,Lithodytes_lineatus_632)\n,(Leptodactylus_fuscus_TJ50,(Leptodactylus_ocellatus_568\n,Vanzolinius_discodactylus_TJ81))))))),(((Telmatobius_simonsi_314\n,(Telmatobius_cf_jahuira_313,Telmatobius_sp_315))\n,((Atelognatus_patagonicus_656,Batrachyla_leptopus_655)\n,(Lepidobatrachus_laevis_939,(Ceratophrys_cranwelli_539\n,Chacophrys_pierottii_1184)))),(((Crossodactylus_schmidti_149\n,(Hylodes_phyllodes_889,Megaelosia_goeldii_611))\n,((Cycloramphus_boraceiensis_890,Rhinoderma_darwinii_1115)\n,((Hylorina_sylvatica,(Alsodes_gargola_653,Eupsophus_calcaratus_657))\n,(Limnomedusa_macroglossa_681,(Proceratophrys_avelinoi_306\n,(Odontophrynus_achalensis_869,Odontophrynus_americanus_309))))))\n,((Thoropa_miliaris_1186,((Mannophryne_trinitatis_609\n,(Allobates_femoralis_394,Colostethus_undulatus_332))\n,((Ameerega_boulengeri_280,Phobobates_silverstonei_646)\n,(Phyllobates_lugubris_329,(Dendrobates_auratus_327,Minyobates_claudiae_324))\n))),(Melanophryniscus_klappenbachi_217,((Osornophryne_guacamayo\n,(Atelopus_zeteki_1039,(Atelopus_flavescens_1046,Atelopus_spumarius_1047)))\n,(Dendrophryniscus_minutus_532,((Bufo_guttatus_TJ2,Bufo_haematiticus_956)\n,((Wolterstorffina_parvipalmata_TJ110,(Werneria_mertensi_TJ114\n,(Nectophryne_afra_TJ124,Nectophryne_batesi_958))),((Bufo_asper_935\n,Pedostibes_hosei_953),((((Ansonia_longidigitata_TJ106,Ansonia_muelleri)\n,(Didynamipus_sjostedti,Nectophrynoides_tornieri_TJ60)),((Pelophryne_brevipes\n,(Bufo_margaritifer,Rhamphophryne_festae)),(Bufo_celebensis\n,(Bufo_galeatus_TJ20,(Bufo_biporcatus,Bufo_divergens_936)))))\n,((Bufo_viridis_1063,(Bufo_melanostictus_TJ10,(Bufo_lemur_1058\n,Schismaderma_carens_TJ73))),((Bufo_bufo,(Bufo_andrewsi_1016\n,Torrentophryne_aspinia)),(((Capensibufo_rosei,Capensibufo_tradouwi)\n,((Bufo_angusticeps,Stephopaedes_anotis),(Bufo_brauni_TJ63\n,(Bufo_tuberosus_TJ127,((Bufo_latifrons_TJ108,Bufo_maculatus_TJ34)\n,(Bufo_camerunensis_TJ121,(Bufo_gutturalis_TJ84,Bufo_regularis_952)))))))\n,((Bufo_boreas_967,(Bufo_punctatus_949,(Bufo_quercicus_940,(Bufo_cognatus_946\n,(Bufo_terrestris_945,Bufo_woodhousii_974))))),(((Bufo_alvarius_1054\n,Bufo_coniferus_955),(Bufo_mazatlanensis,Bufo_nebulifer))\n,(Bufo_variegatus_951,((Bufo_granulosus_TJ1,Bufo_spinulosus_433)\n,(Bufo_amboroensis_TJ32,(Bufo_arenarum_567,(Bufo_marinus_523\n,Bufo_paracnemis_564))))))))))))))))))))))))))))))))))))));\n(Latimeria_chalumnae_1114,(((Didelphis_marsupialis_1092\n,Gazella_thomsoni_1093),((Alligator_sinensis_1090,Iguana_iguana_1001)\n,(Chelydra_serpentina_1091,Pelomedusa_subrufa_1051))),(((Epicrionops_sp_917\n,Rhinatrema_bivittatum_TJ29),((Ichthyophis_sp_TJ102\n,(Ichthyophis_peninsularis_878,Uraeotyphlus_narayani_882))\n,((Boulengerula_uluguruensis_879,Herpele_squalostoma_TJ122)\n,((Caecilia_tentaculata_TJ52,Typhlonectes_natans_877)\n,((Crotaphatrema_tchabalmbaboensis_TJ118,Scolecomorphus_vittatus_TJ104)\n,((Geotrypetes_seraphini_TJ103,(Dermophis_oaxacae_TJ99\n,Schistometopum_gregorii_881)),(Gegeneophis_ramaswamii\n,(Hypogeophis_rostratus_918,Siphonops_hardyi_880))))))))\n,((((Batrachuperus_pinchoni_TJ105,Ranodon_sibiricus)\n,(Cryptobranchus_alleganiensis_1050,(Andrias_davidianus\n,Andrias_japonicus_1059))),((((Necturus_alabamensis_938\n,Necturus_maculosus_TJ6),(Pseudobranchus_striatus_969,(Siren_intermedia\n,Siren_lacertina_968))),(((Dicamptodon_aterrimus_909\n,Dicamptodon_tenebrosus_1048),(Ambystoma_cingulatum_970\n,(Ambystoma_mexicanum_996,Ambystoma_tigrinum_TJ53)))\n,(Salamandra_salamandra_TJ88,((Pleurodeles_waltl_TJ91\n,Tylototriton_shanjing_TJ4),((Notophthalmus_viridiscens_TJ7,Taricha_sp_TJ90)\n,((Pachytriton_brevipes_TJ92,Paramesotriton_sp_TJ76),(Neurergus_crocatus\n,(Euproctus_asper,Triturus_sp_TJ89)))))))),(Rhyacotriton_cascadae_900\n,(Amphiuma_tridactylum_910,((Plethodon_dunni_1049,((Ensatina_eschscholtzii\n,Plethodon_jordani_915),(Aneides_hardii,((Desmognathus_quadramaculatus_1040\n,Desmognathus_wrighti),(Phaeognathus_hubrichti\n,(Hydromantes_platycephalus_1013,Speleomantes_italicus))))))\n,((Batrachoseps_attenuatus,Batrachoseps_wrightorum)\n,(Hemidactylum_scutatum_911,((Eurycea_wilderae_1041\n,Gyrinophilus_porphyriticus_1042),((Nototriton_abscondens,(Oedipina_uniformis\n,(Cryptotriton_alvarezdeltoroi,Dendrotriton_rabbi))),(Thorius_sp_TJ100\n,((Bolitoglossa_rufescens_TJ101,Parvimolge_townsendi),(Ixalotriton_niger\n,(Lineatriton_lineolus,Pseudoeurycea_conanti_TJ98)))))))))))))\n,((Ascaphus_truei_907,(Leiopelma_archeyi_998,Leiopelma_hochstetteri_999))\n,((Rhinophrynus_dorsalis_899,(Hymenochirus_boettgeri,((Pipa_carvalhoi_1038\n,Pipa_pipa_457),(Silurana_tropicalis_TJ128,(Xenopus_gilli_TJ9,Xenopus_laevis)\n)))),(((Alytes_obstetricans_902,(Discoglossus_galganoi_1029\n,Discoglossus_pictus_TJ83)),(Bombina_microdeladigitora_TJ54\n,(Bombina_orientalis_TJ80,(Bombina_bombina_1035,Bombina_variegata_1034))))\n,(((Pelodytes_puntatus_901,(Spea_hammondii_966,(Scaphiopus_couchii_937\n,Scaphiopus_holbrooki_943))),((Pelobates_cultripes,Pelobates_fuscus_903)\n,((Leptolalax_pelodytoides_TJ25,(Leptobrachium_chapaense_450\n,Leptobrachium_hasselti_1022)),(Brachytarsophrys_feae,((Xenophrys_major\n,Xenophrys_major_TJ19),(Megophrys_nasuta_TJ107,(Ophryophryne_microstoma_TJ36\n,Ophryophryne_poilani_TJ21))))))),((Heleophryne_purcelli_633\n,Heleophryne_regis_906),((((Kalophrynus_pleurostigma_933\n,(Synapturanus_mirandaribeiroi_530,((Micryletta_inornata\n,Phrynomantis_bifasciatus_941),((((Hoplophryne_rogersi_TJ68\n,Ramanella_obscura),((Anodonthyla_montana,Platypelis_sp_TJ58)\n,(Plethodontohyla_sp_TJ56,Stumpffia_sp_TJ59))),((Ctenophryne_geayei_TJ27\n,Nelsonophryne_aequatorialis),(Dasypops_schirchi_888\n,(Hamptophryne_boliviana_TJ86,(Elachistocleis_ovalis_TJ51\n,(Dermatonotus_muelleri_1185,(Gastrophryne_elegans_TJ74\n,Gastrophryne_olivacea_1053))))))),((Scaphiophryne_marmorata_TJ57\n,(Kaloula_pulchra_TJ41,(Chaperina_fusca_932,(Calluella_guttulata_931\n,(Microhyla_heymonsi_TJ26,Microhyla_sp_TJ70))))),(Dyscophus_guineti_TJ82\n,((Choerophryne_sp_991,Cophixalus_sphagnicola_990),((Genyophryne_thomsoni_993\n,(Copiula_sp_992,Sphenophryne_sp_989)),(Liophryne_rhododactyla_983\n,(Aphantophryne_pansa_980,(Callulops_slateri,Oreophryne_brachypus_979))))))))\n))),((Hemisus_marmoratus_TJ78,(Breviceps_mossambicus_942\n,(Probreviceps_macrodactylus_TJ69,(Callulina_kisiwamsitu_TJ77\n,Callulina_kreffti)))),(((Acanthixalus_spinosus,(Kassina_senegalensis_TJ85\n,Phlyctimantis_leonardi_TJ119)),(Opisthothylax_immaculatus_962\n,(((Afrixalus_fornasinii_TJ44,Afrixalus_pygmaeus_1019)\n,(Tachycnemis_seychellensis_TJ95,(Heterixalus_sp_TJ93,Heterixalus_tricolor)))\n,(Cryptothylax_gresshoffi_959,((Alexteroon_obstetricans_960\n,Alexteroon_obstetricans_TJ109),(Hyperolius_tuberilinguis_TJ43\n,(Hyperolius_alticola_1011,(Hyperolius_punticulatus_TJ35\n,Nesionixalus_thomensis_1017)))))))),((Leptopelis_argenteus_1012\n,(Leptopelis_bocagei_TJ67,(Leptopelis_sp_950,Leptopelis_vermiculatus_1026)))\n,((Leptodactylodon_bicolor_TJ129,(Nyctibates_corrugatus_TJ126\n,(Astylosternus_schiotzi_TJ116,Trichobatrachus_robustus_TJ111)))\n,(Scotobleps_gabonicus_TJ130,((Cardioglossa_gratiosa_964\n,Cardioglossa_leucomystax_845),((Schoutedenella_sylvatica_844\n,Schoutedenella_taeniata_1018),((Arthroleptis_tanneri_TJ75\n,Arthroleptis_variabilis_847),(Schoutedenella_schubotzi_1021\n,Schoutedenella_xenodactyloides_TJ79))))))))))\n,((Ptychadena_mascareniensis_181,(Ptychadena_anchietae\n,Ptychadena_cooperi_588)),((Ingerana_baluensis_929,(Discodeles_guppyi_984\n,(Ceratobatrachus_guentheri_982,(Batrachylodes_vertebralis_994\n,(Platymantis_pelewensis_896,Platymantis_weberi_981))))),((Micrixalus_fuscus\n,Micrixalus_kottigeharensis),((((Phrynobatrachus_dendrobates_1015\n,Phrynodon_sandersoni_848),((Dimorphognathus_africanus_963\n,(Phrynobatrachus_auritus_849,Phrynobatrachus_natalensis_TJ61))\n,(Phrynobatrachus_calcaratus_1024,(Phrynobatrachus_dispar_1009\n,Phrynobatrachus_mababiensis_TJ72)))),(((Conraua_goliath_919\n,Conraua_robusta_TJ113),((Indirana_sp1_FB2000a,Indirana_sp2_FB2000b)\n,(Arthroleptides_sp_TJ62,(Petropedetes_palmipes_841,(Petropedetes_newtoni_965\n,(Petropedetes_cameronensis_843,Petropedetes_parkeri))))))\n,((Pyxicephalus_edulis_944,(Aubria_subsigillata_961\n,Aubria_subsigillata_TJ117)),(Tomopterna_delalandii_TJ5\n,((Arthroleptella_bicolor_591,Natalobatrachus_bonebergi)\n,((Afrana_fuscigula_590,(Afrana_angolensis_1014,Amietia_vertebralis_TJ45))\n,(Strongylopus_grayii_589,(Anhydrophryne_rattrayi,Cacosternum_platys_1045))))\n)))),(((Micrixalus_borealis_1020,(Occidozyga_baluensis_930\n,(Occidozyga_laevis_TJ12,Occidozyga_lima_1010))),((Limnonectes_kuhlii_TJ14\n,(Limnonectes_grunniens_986,(Limnonectes_blythi_TJ22,(Taylorana_limborgi\n,(Limnonectes_acanthi,(Limnonectes_heinrichi,Limnonectes_visayanus))))))\n,((Paa_verrucospinosa_TJ23,Quasipaa_exilispinosa_1030),(Nanorana_pleskei\n,((Fejervarya_cancrivorus,Fejervarya_limnocharis_TJ15)\n,((Sphaerotheca_breviceps_893,Sphaerotheca_pluvialis)\n,((Fejervarya_kirtisinghei,Fejervarya_syhadrensis),(Nannophrys_ceylonensis\n,(Euphlyctis_cyanophlyctis,(Hoplobatrachus_occipitalis_513\n,Hoplobatrachus_rugulosus_928)))))))))),((((Boophis_albilabris_185\n,Boophis_tephraeomystax_182),((Aglyptodactylus_madagascariensis_505\n,Laliostoma_labrosum_508),((Mantella_aurantiaca_238,Mantella_nigricans_204)\n,(Mantidactylus_cf_femoralis_187,Mantidactylus_peraccae_272))))\n,(Buergeria_japonica_502,(Philautus_gracilipes_446\n,((Chirixalus_eiffingeri_912,Chirixalus_idiooticus_500),(((Nyctixalus_905\n,Nyctixalus_pictus_920),(Philautus_rhododiscus_TJ37,Theloderma_corticale_445)\n),((Rhacophorus_annamensis_441,(Rhacophorus_bipunctatus_440\n,(Rhacophorus_calcaneus_TJ24,Rhacophorus_orlovi_443))),((Polypedates_cruciger\n,Polypedates_leucomystax_442),(Chirixalus_vittatus_921,(Chirixalus_doriae_922\n,Chiromantis_xerampelina_TJ42))))))))),((Lankanectes_corrugatus\n,(Nyctibatrachus_cf_aliciae,Nyctibatrachus_major)),(Staurois_tuberlinguis_927\n,((Sylvirana_guentheri_1052,(Hylarana_erythraea_925\n,Hylarana_taipehensis_TJ40)),(((Chalcorana_chalconota_926\n,(Amnirana_albilabris_TJ131,Amnirana_galamensis_512))\n,((Sylvirana_maosonensis_TJ18,Sylvirana_nigrovittata_TJ16)\n,(Sylvirana_temporalis,(Papurana_daemeli_985,Tylerana_arfaki_987))))\n,((Clinotarsus_curtipes,Meristogenys_orphnocnemis_934)\n,((Amolops_hongkongensis,(Pelophylax_nigromaculata_924,Pelophylax_ridibunda))\n,(Glandirana_minima,(((Nidirana_adenopleura_908,Nidirana_chapaensis_TJ13)\n,((Amolops_chapaensis_TJ17,Odorrana_grahami_1025),(Huia_nasica_TJ11\n,Odorrana_livida_TJ38))),(((Amerana_mucosa_976,Aurorana_aurora_975)\n,(Pseudorana_johnsi_997,(Rana_japonica_923,(Pseudoamalops_sauteri_914\n,Rana_temporaria_916)))),((Aquarana_grylio_972,(Aquarana_heckscheri_977\n,(Aquarana_catesbeiana_1044,Aquarana_clamitans_971))),(Rana_sylvatica_TJ33\n,((Lithobates_palmipes_TJ28,(Sierrana_maculata_1076\n,Trypheropsis_warszewitschii_1043)),(Pantherana_capito_973\n,((Pantherana_chiricahuensis_1055,Pantherana_pipiens_913)\n,(Pantherana_berlandieri,(Pantherana_forreri_895\n,Pantherana_yavapaiensis_1057))))))))))))))))))))))),(((Nasikabatrachidae_sp\n,Nasikabatrachus_sahyadrensis),(Nesomantis_thomasseti_TJ96\n,Sooglossus_sechellensis_TJ94)),(((Caudiverbera_caudiverbera_TJ87\n,Telmatobufo_venustus_1131),((Kyarranus_sphagnicolus_1084\n,(Adelotus_brevis_1073,(((Neobatrachus_pictus_1070,Neobatrachus_sudelli_673)\n,(Notaden_melanoscaphus_1068,(Lechriodus_fletcheri_1065\n,Limnodynastes_ornatus_1064))),(Heleioporus_australiacus_1079\n,(Limnodynastes_dumerilli_1067,((Limnodynastes_depressus_1080\n,Limnodynastes_peronii_1032),(Limnodynastes_salmini\n,Megistolotis_lignarius_1069))))))),((Mixophyes_carbinensis_1086\n,Rheobatrachus_silus_1061),(Taudactylus_acutirostris_1062\n,(((Bryobatrachus_nimbus_1074,Crinia_signifera_978),(Paracrinia_haswelli_1077\n,(Assa_darlingtoni_1066,Geocrinia_victoriana_1072)))\n,((Spicospina_flammocaerulea_1075,Uperoleia_laevigata_1003)\n,((Pseudophryne_bibroni_677,Pseudophryne_coriacea_1082)\n,(Myobatachus_gouldii_1081,(Arenophryne_sp_1155,Metacrinia_nichollsi_1071))))\n))))),(Hemiphractus_helioi_467,((((Eleutherodactylus_binotatus_884\n,Ischnocnema_sp_521),(Barycholos_ternetzi_887,(Brachycephalus_ephippium_883\n,Eleutherodactylus_juipoca_886))),((Craugastor_pluvicanorus_TJ31\n,(Euhyas_planirostris_898,(Syrrhophus_marnockii_894,Syrrhophus_nitidus_1087))\n),((Phrynopus_sp_KU_202652,Phrynopus_sp_TJ30),(Craugastor_bufoniformis_954\n,((Craugastor_alfredi_1089,Craugastor_augusti_1056),(Craugastor_rhodopis_1088\n,(Craugastor_punctariolus_957,Craugastor_ranoides_897)))))))\n,((Cryptobatrachus_sp,Stefania_evansi_417),((Flectonotus_sp_690\n,(Gastrotheca_cf_marsupiata_317,Gastrotheca_fissipes_825))\n,(((((Agalychnis_calcarifer_1006,Phyllomedusa_vaillanti_103)\n,(Agalychnis_callidryas_TJ71,Phasmahyla_guttata_687)),((Litoria_meiriana_675\n,(Litoria_freycineti_672,Litoria_inermis_995)),(Nyctimistes_pulchra_676\n,((Litoria_nannotis_1000,Nyctimystes_dayi_1002),((Cyclorana_australis_674\n,Litoria_aurea_543),(Litoria_genimaculata_1004,Litoria_lesueurii_988))))))\n,(((Sphaenorhynchus_lacteus_138,(Scinax_garbei_90,Scinax_ruber_16))\n,((Hyloscirtus_armata_318,Hyloscirtus_palmeri_504),(Hypsiboas_granosus_416\n,((Aplastodiscus_perviridis_4,Hypsiboas_albomarginata_140)\n,(Hypsiboas_boans_486,Hypsiboas_multifasciata_102)))))\n,(((Scarthyla_goinorum_86,(Lysapsus_laevis_629,Pseudis_paradoxa_704))\n,(Dendropsophus_minutus_35,(Dendropsophus_marmoratus_468\n,(Dendropsophus_nana_172,Dendropsophus_parviceps_80))))\n,((Phyllodytes_luteolus_823,((Osteocephalus_cf_taurinus_410\n,Osteopilus_septentrionalis_139),(Argenteohyla_siemersi_pederseni_292\n,(Trachycephalus_jordani_540,Trachycephalus_venulosus_94))))\n,((Ecnomiohyla_miliaria_639,(Duellmanohyla_rufioculis_211\n,Ptychohyla_leonhardschultzei_796)),(Charadrahyla_nephila_551\n,(((Exerodonta_chimalapa_549,Plectrohyla_guatemalensis_802)\n,(Acris_crepitans_604,(Pseudacris_crucifer_638,Pseudacris_triseriata_833)))\n,((Hyla_arborea_871,Isthmohyla_rivularis_210),((Hyla_cinerea_207\n,Tlalocohyla_picta_658),(Smilisca_phaeota_459,(Anotheca_spinosa_552\n,Triprion_petasatus_458))))))))))),(((Allophryne_ruthveni_837\n,(Hyalinobatrachium_fleischmanni_TJ97,(Centrolene_prosoblepon_827\n,(Centrolene_geckoideum,Cochranella_bejaranoi_311))))\n,((Pleurodema_brachyops_630,(Edalorhina_perezi_531,Physalaemus_cuvieri_TJ65))\n,(Pseudopaludicola_sp_650,((Paratelmatobius_sp_891,Scythrophrys_sawayae_892)\n,((Adenomera_hylaedactyla_529,Lithodytes_lineatus_632)\n,(Leptodactylus_fuscus_TJ50,(Leptodactylus_ocellatus_568\n,Vanzolinius_discodactylus_TJ81))))))),(((Telmatobius_simonsi_314\n,(Telmatobius_cf_jahuira_313,Telmatobius_sp_315))\n,((Atelognatus_patagonicus_656,Batrachyla_leptopus_655)\n,(Lepidobatrachus_laevis_939,(Ceratophrys_cranwelli_539\n,Chacophrys_pierottii_1184)))),(((Crossodactylus_schmidti_149\n,(Hylodes_phyllodes_889,Megaelosia_goeldii_611))\n,((Cycloramphus_boraceiensis_890,Rhinoderma_darwinii_1115)\n,((Hylorina_sylvatica,(Alsodes_gargola_653,Eupsophus_calcaratus_657))\n,(Limnomedusa_macroglossa_681,(Proceratophrys_avelinoi_306\n,(Odontophrynus_achalensis_869,Odontophrynus_americanus_309))))))\n,((Thoropa_miliaris_1186,((Mannophryne_trinitatis_609\n,(Allobates_femoralis_394,Colostethus_undulatus_332))\n,((Ameerega_boulengeri_280,Phobobates_silverstonei_646)\n,(Phyllobates_lugubris_329,(Dendrobates_auratus_327,Minyobates_claudiae_324))\n))),(Melanophryniscus_klappenbachi_217,((Osornophryne_guacamayo\n,(Atelopus_zeteki_1039,(Atelopus_flavescens_1046,Atelopus_spumarius_1047)))\n,(Dendrophryniscus_minutus_532,((Bufo_guttatus_TJ2,Bufo_haematiticus_956)\n,((Wolterstorffina_parvipalmata_TJ110,(Werneria_mertensi_TJ114\n,(Nectophryne_afra_TJ124,Nectophryne_batesi_958))),((Bufo_asper_935\n,Pedostibes_hosei_953),((((Ansonia_longidigitata_TJ106,Ansonia_muelleri)\n,(Didynamipus_sjostedti,Nectophrynoides_tornieri_TJ60)),((Pelophryne_brevipes\n,(Bufo_margaritifer,Rhamphophryne_festae)),(Bufo_celebensis\n,(Bufo_galeatus_TJ20,(Bufo_biporcatus,Bufo_divergens_936)))))\n,((Bufo_viridis_1063,(Bufo_melanostictus_TJ10,(Bufo_lemur_1058\n,Schismaderma_carens_TJ73))),((Bufo_bufo,(Bufo_andrewsi_1016\n,Torrentophryne_aspinia)),(((Capensibufo_rosei,Capensibufo_tradouwi)\n,((Bufo_angusticeps,Stephopaedes_anotis),(Bufo_brauni_TJ63\n,(Bufo_tuberosus_TJ127,((Bufo_latifrons_TJ108,Bufo_maculatus_TJ34)\n,(Bufo_camerunensis_TJ121,(Bufo_gutturalis_TJ84,Bufo_regularis_952)))))))\n,((Bufo_boreas_967,(Bufo_punctatus_949,(Bufo_quercicus_940,(Bufo_cognatus_946\n,(Bufo_terrestris_945,Bufo_woodhousii_974))))),(((Bufo_alvarius_1054\n,Bufo_coniferus_955),(Bufo_mazatlanensis,Bufo_nebulifer))\n,(Bufo_variegatus_951,((Bufo_granulosus_TJ1,Bufo_spinulosus_433)\n,(Bufo_amboroensis_TJ32,(Bufo_arenarum_567,(Bufo_marinus_523\n,Bufo_paracnemis_564))))))))))))))))))))))))))))))))))))));\n(Latimeria_chalumnae_1114,(((Didelphis_marsupialis_1092\n,Gazella_thomsoni_1093),((Alligator_sinensis_1090,Iguana_iguana_1001)\n,(Chelydra_serpentina_1091,Pelomedusa_subrufa_1051))),(((Epicrionops_sp_917\n,Rhinatrema_bivittatum_TJ29),((Ichthyophis_sp_TJ102\n,(Ichthyophis_peninsularis_878,Uraeotyphlus_narayani_882))\n,((Boulengerula_uluguruensis_879,Herpele_squalostoma_TJ122)\n,((Caecilia_tentaculata_TJ52,Typhlonectes_natans_877)\n,((Crotaphatrema_tchabalmbaboensis_TJ118,Scolecomorphus_vittatus_TJ104)\n,((Geotrypetes_seraphini_TJ103,(Dermophis_oaxacae_TJ99\n,Schistometopum_gregorii_881)),(Gegeneophis_ramaswamii\n,(Hypogeophis_rostratus_918,Siphonops_hardyi_880))))))))\n,((((Batrachuperus_pinchoni_TJ105,Ranodon_sibiricus)\n,(Cryptobranchus_alleganiensis_1050,(Andrias_davidianus\n,Andrias_japonicus_1059))),((((Necturus_alabamensis_938\n,Necturus_maculosus_TJ6),(Pseudobranchus_striatus_969,(Siren_intermedia\n,Siren_lacertina_968))),(((Dicamptodon_aterrimus_909\n,Dicamptodon_tenebrosus_1048),(Ambystoma_cingulatum_970\n,(Ambystoma_mexicanum_996,Ambystoma_tigrinum_TJ53)))\n,(Salamandra_salamandra_TJ88,((Pleurodeles_waltl_TJ91\n,Tylototriton_shanjing_TJ4),((Notophthalmus_viridiscens_TJ7,Taricha_sp_TJ90)\n,((Pachytriton_brevipes_TJ92,Paramesotriton_sp_TJ76),(Neurergus_crocatus\n,(Euproctus_asper,Triturus_sp_TJ89)))))))),(Rhyacotriton_cascadae_900\n,(Amphiuma_tridactylum_910,((Plethodon_dunni_1049,((Ensatina_eschscholtzii\n,Plethodon_jordani_915),(Aneides_hardii,((Desmognathus_quadramaculatus_1040\n,Desmognathus_wrighti),(Phaeognathus_hubrichti\n,(Hydromantes_platycephalus_1013,Speleomantes_italicus))))))\n,((Batrachoseps_attenuatus,Batrachoseps_wrightorum)\n,(Hemidactylum_scutatum_911,((Eurycea_wilderae_1041\n,Gyrinophilus_porphyriticus_1042),((Nototriton_abscondens,(Oedipina_uniformis\n,(Cryptotriton_alvarezdeltoroi,Dendrotriton_rabbi))),(Thorius_sp_TJ100\n,((Bolitoglossa_rufescens_TJ101,Parvimolge_townsendi),(Ixalotriton_niger\n,(Lineatriton_lineolus,Pseudoeurycea_conanti_TJ98)))))))))))))\n,((Ascaphus_truei_907,(Leiopelma_archeyi_998,Leiopelma_hochstetteri_999))\n,((Rhinophrynus_dorsalis_899,(Hymenochirus_boettgeri,((Pipa_carvalhoi_1038\n,Pipa_pipa_457),(Silurana_tropicalis_TJ128,(Xenopus_gilli_TJ9,Xenopus_laevis)\n)))),(((Alytes_obstetricans_902,(Discoglossus_galganoi_1029\n,Discoglossus_pictus_TJ83)),(Bombina_microdeladigitora_TJ54\n,(Bombina_orientalis_TJ80,(Bombina_bombina_1035,Bombina_variegata_1034))))\n,(((Pelodytes_puntatus_901,(Spea_hammondii_966,(Scaphiopus_couchii_937\n,Scaphiopus_holbrooki_943))),((Pelobates_cultripes,Pelobates_fuscus_903)\n,((Leptolalax_pelodytoides_TJ25,(Leptobrachium_chapaense_450\n,Leptobrachium_hasselti_1022)),((Megophrys_nasuta_TJ107\n,(Ophryophryne_microstoma_TJ36,Ophryophryne_poilani_TJ21))\n,(Brachytarsophrys_feae,(Xenophrys_major,Xenophrys_major_TJ19))))))\n,((Heleophryne_purcelli_633,Heleophryne_regis_906)\n,((((Kalophrynus_pleurostigma_933,(Synapturanus_mirandaribeiroi_530\n,((Micryletta_inornata,Phrynomantis_bifasciatus_941)\n,((((Hoplophryne_rogersi_TJ68,Ramanella_obscura),((Anodonthyla_montana\n,Platypelis_sp_TJ58),(Plethodontohyla_sp_TJ56,Stumpffia_sp_TJ59)))\n,((Ctenophryne_geayei_TJ27,Nelsonophryne_aequatorialis)\n,(Dasypops_schirchi_888,(Hamptophryne_boliviana_TJ86\n,(Elachistocleis_ovalis_TJ51,(Dermatonotus_muelleri_1185\n,(Gastrophryne_elegans_TJ74,Gastrophryne_olivacea_1053)))))))\n,((Scaphiophryne_marmorata_TJ57,(Kaloula_pulchra_TJ41,(Chaperina_fusca_932\n,(Calluella_guttulata_931,(Microhyla_heymonsi_TJ26,Microhyla_sp_TJ70)))))\n,(Dyscophus_guineti_TJ82,((Choerophryne_sp_991,Cophixalus_sphagnicola_990)\n,((Genyophryne_thomsoni_993,(Copiula_sp_992,Sphenophryne_sp_989))\n,(Liophryne_rhododactyla_983,(Aphantophryne_pansa_980,(Callulops_slateri\n,Oreophryne_brachypus_979))))))))))),((Hemisus_marmoratus_TJ78\n,(Breviceps_mossambicus_942,(Probreviceps_macrodactylus_TJ69\n,(Callulina_kisiwamsitu_TJ77,Callulina_kreffti)))),(((Acanthixalus_spinosus\n,(Kassina_senegalensis_TJ85,Phlyctimantis_leonardi_TJ119))\n,(Opisthothylax_immaculatus_962,(((Afrixalus_fornasinii_TJ44\n,Afrixalus_pygmaeus_1019),(Tachycnemis_seychellensis_TJ95\n,(Heterixalus_sp_TJ93,Heterixalus_tricolor))),(Cryptothylax_gresshoffi_959\n,((Alexteroon_obstetricans_960,Alexteroon_obstetricans_TJ109)\n,(Hyperolius_tuberilinguis_TJ43,(Hyperolius_alticola_1011\n,(Hyperolius_punticulatus_TJ35,Nesionixalus_thomensis_1017))))))))\n,((Leptopelis_argenteus_1012,(Leptopelis_bocagei_TJ67,(Leptopelis_sp_950\n,Leptopelis_vermiculatus_1026))),((Leptodactylodon_bicolor_TJ129\n,(Nyctibates_corrugatus_TJ126,(Astylosternus_schiotzi_TJ116\n,Trichobatrachus_robustus_TJ111))),(Scotobleps_gabonicus_TJ130\n,((Cardioglossa_gratiosa_964,Cardioglossa_leucomystax_845)\n,((Schoutedenella_sylvatica_844,Schoutedenella_taeniata_1018)\n,((Arthroleptis_tanneri_TJ75,Arthroleptis_variabilis_847)\n,(Schoutedenella_schubotzi_1021,Schoutedenella_xenodactyloides_TJ79))))))))))\n,((Ptychadena_mascareniensis_181,(Ptychadena_anchietae\n,Ptychadena_cooperi_588)),((Ingerana_baluensis_929,(Discodeles_guppyi_984\n,(Ceratobatrachus_guentheri_982,(Batrachylodes_vertebralis_994\n,(Platymantis_pelewensis_896,Platymantis_weberi_981))))),((Micrixalus_fuscus\n,Micrixalus_kottigeharensis),((((Phrynobatrachus_dendrobates_1015\n,Phrynodon_sandersoni_848),((Dimorphognathus_africanus_963\n,(Phrynobatrachus_auritus_849,Phrynobatrachus_natalensis_TJ61))\n,(Phrynobatrachus_calcaratus_1024,(Phrynobatrachus_dispar_1009\n,Phrynobatrachus_mababiensis_TJ72)))),(((Conraua_goliath_919\n,Conraua_robusta_TJ113),((Indirana_sp1_FB2000a,Indirana_sp2_FB2000b)\n,(Arthroleptides_sp_TJ62,(Petropedetes_palmipes_841,(Petropedetes_newtoni_965\n,(Petropedetes_cameronensis_843,Petropedetes_parkeri))))))\n,((Pyxicephalus_edulis_944,(Aubria_subsigillata_961\n,Aubria_subsigillata_TJ117)),(Tomopterna_delalandii_TJ5\n,((Arthroleptella_bicolor_591,Natalobatrachus_bonebergi)\n,((Afrana_fuscigula_590,(Afrana_angolensis_1014,Amietia_vertebralis_TJ45))\n,(Strongylopus_grayii_589,(Anhydrophryne_rattrayi,Cacosternum_platys_1045))))\n)))),(((Micrixalus_borealis_1020,(Occidozyga_baluensis_930\n,(Occidozyga_laevis_TJ12,Occidozyga_lima_1010))),((Limnonectes_kuhlii_TJ14\n,(Limnonectes_grunniens_986,(Limnonectes_blythi_TJ22,(Taylorana_limborgi\n,(Limnonectes_acanthi,(Limnonectes_heinrichi,Limnonectes_visayanus))))))\n,((Paa_verrucospinosa_TJ23,Quasipaa_exilispinosa_1030),(Nanorana_pleskei\n,((Fejervarya_cancrivorus,Fejervarya_limnocharis_TJ15)\n,((Sphaerotheca_breviceps_893,Sphaerotheca_pluvialis)\n,((Fejervarya_kirtisinghei,Fejervarya_syhadrensis),(Nannophrys_ceylonensis\n,(Euphlyctis_cyanophlyctis,(Hoplobatrachus_occipitalis_513\n,Hoplobatrachus_rugulosus_928)))))))))),((((Boophis_albilabris_185\n,Boophis_tephraeomystax_182),((Aglyptodactylus_madagascariensis_505\n,Laliostoma_labrosum_508),((Mantella_aurantiaca_238,Mantella_nigricans_204)\n,(Mantidactylus_cf_femoralis_187,Mantidactylus_peraccae_272))))\n,(Buergeria_japonica_502,(Philautus_gracilipes_446\n,((Chirixalus_eiffingeri_912,Chirixalus_idiooticus_500),(((Nyctixalus_905\n,Nyctixalus_pictus_920),(Philautus_rhododiscus_TJ37,Theloderma_corticale_445)\n),((Rhacophorus_annamensis_441,(Rhacophorus_bipunctatus_440\n,(Rhacophorus_calcaneus_TJ24,Rhacophorus_orlovi_443))),((Polypedates_cruciger\n,Polypedates_leucomystax_442),(Chirixalus_vittatus_921,(Chirixalus_doriae_922\n,Chiromantis_xerampelina_TJ42))))))))),((Lankanectes_corrugatus\n,(Nyctibatrachus_cf_aliciae,Nyctibatrachus_major)),(Staurois_tuberlinguis_927\n,((Sylvirana_guentheri_1052,(Hylarana_erythraea_925\n,Hylarana_taipehensis_TJ40)),(((Chalcorana_chalconota_926\n,(Amnirana_albilabris_TJ131,Amnirana_galamensis_512))\n,((Sylvirana_maosonensis_TJ18,Sylvirana_nigrovittata_TJ16)\n,(Sylvirana_temporalis,(Papurana_daemeli_985,Tylerana_arfaki_987))))\n,((Clinotarsus_curtipes,Meristogenys_orphnocnemis_934)\n,((Amolops_hongkongensis,(Pelophylax_nigromaculata_924,Pelophylax_ridibunda))\n,(Glandirana_minima,(((Nidirana_adenopleura_908,Nidirana_chapaensis_TJ13)\n,((Amolops_chapaensis_TJ17,Odorrana_grahami_1025),(Huia_nasica_TJ11\n,Odorrana_livida_TJ38))),(((Amerana_mucosa_976,Aurorana_aurora_975)\n,(Pseudorana_johnsi_997,(Rana_japonica_923,(Pseudoamalops_sauteri_914\n,Rana_temporaria_916)))),((Aquarana_grylio_972,(Aquarana_heckscheri_977\n,(Aquarana_catesbeiana_1044,Aquarana_clamitans_971))),(Rana_sylvatica_TJ33\n,((Lithobates_palmipes_TJ28,(Sierrana_maculata_1076\n,Trypheropsis_warszewitschii_1043)),(Pantherana_capito_973\n,((Pantherana_chiricahuensis_1055,Pantherana_pipiens_913)\n,(Pantherana_berlandieri,(Pantherana_forreri_895\n,Pantherana_yavapaiensis_1057))))))))))))))))))))))),(((Nasikabatrachidae_sp\n,Nasikabatrachus_sahyadrensis),(Nesomantis_thomasseti_TJ96\n,Sooglossus_sechellensis_TJ94)),(((Caudiverbera_caudiverbera_TJ87\n,Telmatobufo_venustus_1131),((Kyarranus_sphagnicolus_1084\n,(Adelotus_brevis_1073,(((Neobatrachus_pictus_1070,Neobatrachus_sudelli_673)\n,(Notaden_melanoscaphus_1068,(Lechriodus_fletcheri_1065\n,Limnodynastes_ornatus_1064))),(Heleioporus_australiacus_1079\n,(Limnodynastes_dumerilli_1067,((Limnodynastes_depressus_1080\n,Limnodynastes_peronii_1032),(Limnodynastes_salmini\n,Megistolotis_lignarius_1069))))))),((Mixophyes_carbinensis_1086\n,Rheobatrachus_silus_1061),(Taudactylus_acutirostris_1062\n,(((Bryobatrachus_nimbus_1074,Crinia_signifera_978),(Paracrinia_haswelli_1077\n,(Assa_darlingtoni_1066,Geocrinia_victoriana_1072)))\n,((Spicospina_flammocaerulea_1075,Uperoleia_laevigata_1003)\n,((Pseudophryne_bibroni_677,Pseudophryne_coriacea_1082)\n,(Myobatachus_gouldii_1081,(Arenophryne_sp_1155,Metacrinia_nichollsi_1071))))\n))))),(Hemiphractus_helioi_467,((((Eleutherodactylus_binotatus_884\n,Ischnocnema_sp_521),(Barycholos_ternetzi_887,(Brachycephalus_ephippium_883\n,Eleutherodactylus_juipoca_886))),((Craugastor_pluvicanorus_TJ31\n,(Euhyas_planirostris_898,(Syrrhophus_marnockii_894,Syrrhophus_nitidus_1087))\n),((Phrynopus_sp_KU_202652,Phrynopus_sp_TJ30),(Craugastor_bufoniformis_954\n,((Craugastor_alfredi_1089,Craugastor_augusti_1056),(Craugastor_rhodopis_1088\n,(Craugastor_punctariolus_957,Craugastor_ranoides_897)))))))\n,((Cryptobatrachus_sp,Stefania_evansi_417),((Flectonotus_sp_690\n,(Gastrotheca_cf_marsupiata_317,Gastrotheca_fissipes_825))\n,(((((Agalychnis_calcarifer_1006,Phyllomedusa_vaillanti_103)\n,(Agalychnis_callidryas_TJ71,Phasmahyla_guttata_687)),((Litoria_meiriana_675\n,(Litoria_freycineti_672,Litoria_inermis_995)),(Nyctimistes_pulchra_676\n,((Litoria_nannotis_1000,Nyctimystes_dayi_1002),((Cyclorana_australis_674\n,Litoria_aurea_543),(Litoria_genimaculata_1004,Litoria_lesueurii_988))))))\n,(((Sphaenorhynchus_lacteus_138,(Scinax_garbei_90,Scinax_ruber_16))\n,((Hyloscirtus_armata_318,Hyloscirtus_palmeri_504),(Hypsiboas_granosus_416\n,((Aplastodiscus_perviridis_4,Hypsiboas_albomarginata_140)\n,(Hypsiboas_boans_486,Hypsiboas_multifasciata_102)))))\n,(((Scarthyla_goinorum_86,(Lysapsus_laevis_629,Pseudis_paradoxa_704))\n,(Dendropsophus_minutus_35,(Dendropsophus_marmoratus_468\n,(Dendropsophus_nana_172,Dendropsophus_parviceps_80))))\n,((Phyllodytes_luteolus_823,((Osteocephalus_cf_taurinus_410\n,Osteopilus_septentrionalis_139),(Argenteohyla_siemersi_pederseni_292\n,(Trachycephalus_jordani_540,Trachycephalus_venulosus_94))))\n,((Ecnomiohyla_miliaria_639,(Duellmanohyla_rufioculis_211\n,Ptychohyla_leonhardschultzei_796)),(Charadrahyla_nephila_551\n,(((Exerodonta_chimalapa_549,Plectrohyla_guatemalensis_802)\n,(Acris_crepitans_604,(Pseudacris_crucifer_638,Pseudacris_triseriata_833)))\n,((Hyla_arborea_871,Isthmohyla_rivularis_210),((Hyla_cinerea_207\n,Tlalocohyla_picta_658),(Smilisca_phaeota_459,(Anotheca_spinosa_552\n,Triprion_petasatus_458))))))))))),(((Allophryne_ruthveni_837\n,(Hyalinobatrachium_fleischmanni_TJ97,(Centrolene_prosoblepon_827\n,(Centrolene_geckoideum,Cochranella_bejaranoi_311))))\n,((Pleurodema_brachyops_630,(Edalorhina_perezi_531,Physalaemus_cuvieri_TJ65))\n,(Pseudopaludicola_sp_650,((Paratelmatobius_sp_891,Scythrophrys_sawayae_892)\n,((Adenomera_hylaedactyla_529,Lithodytes_lineatus_632)\n,(Leptodactylus_fuscus_TJ50,(Leptodactylus_ocellatus_568\n,Vanzolinius_discodactylus_TJ81))))))),(((Telmatobius_simonsi_314\n,(Telmatobius_cf_jahuira_313,Telmatobius_sp_315))\n,((Atelognatus_patagonicus_656,Batrachyla_leptopus_655)\n,(Lepidobatrachus_laevis_939,(Ceratophrys_cranwelli_539\n,Chacophrys_pierottii_1184)))),(((Crossodactylus_schmidti_149\n,(Hylodes_phyllodes_889,Megaelosia_goeldii_611))\n,((Cycloramphus_boraceiensis_890,Rhinoderma_darwinii_1115)\n,((Hylorina_sylvatica,(Alsodes_gargola_653,Eupsophus_calcaratus_657))\n,(Limnomedusa_macroglossa_681,(Proceratophrys_avelinoi_306\n,(Odontophrynus_achalensis_869,Odontophrynus_americanus_309))))))\n,((Thoropa_miliaris_1186,((Mannophryne_trinitatis_609\n,(Allobates_femoralis_394,Colostethus_undulatus_332))\n,((Ameerega_boulengeri_280,Phobobates_silverstonei_646)\n,(Phyllobates_lugubris_329,(Dendrobates_auratus_327,Minyobates_claudiae_324))\n))),(Melanophryniscus_klappenbachi_217,((Osornophryne_guacamayo\n,(Atelopus_zeteki_1039,(Atelopus_flavescens_1046,Atelopus_spumarius_1047)))\n,(Dendrophryniscus_minutus_532,((Bufo_guttatus_TJ2,Bufo_haematiticus_956)\n,((Wolterstorffina_parvipalmata_TJ110,(Werneria_mertensi_TJ114\n,(Nectophryne_afra_TJ124,Nectophryne_batesi_958))),((Bufo_asper_935\n,Pedostibes_hosei_953),((((Ansonia_longidigitata_TJ106,Ansonia_muelleri)\n,(Didynamipus_sjostedti,Nectophrynoides_tornieri_TJ60)),((Pelophryne_brevipes\n,(Bufo_margaritifer,Rhamphophryne_festae)),(Bufo_celebensis\n,(Bufo_galeatus_TJ20,(Bufo_biporcatus,Bufo_divergens_936)))))\n,((Bufo_viridis_1063,(Bufo_melanostictus_TJ10,(Bufo_lemur_1058\n,Schismaderma_carens_TJ73))),((Bufo_bufo,(Bufo_andrewsi_1016\n,Torrentophryne_aspinia)),(((Capensibufo_rosei,Capensibufo_tradouwi)\n,((Bufo_angusticeps,Stephopaedes_anotis),(Bufo_brauni_TJ63\n,(Bufo_tuberosus_TJ127,((Bufo_latifrons_TJ108,Bufo_maculatus_TJ34)\n,(Bufo_camerunensis_TJ121,(Bufo_gutturalis_TJ84,Bufo_regularis_952)))))))\n,((Bufo_boreas_967,(Bufo_punctatus_949,(Bufo_quercicus_940,(Bufo_cognatus_946\n,(Bufo_terrestris_945,Bufo_woodhousii_974))))),(((Bufo_alvarius_1054\n,Bufo_coniferus_955),(Bufo_mazatlanensis,Bufo_nebulifer))\n,(Bufo_variegatus_951,((Bufo_granulosus_TJ1,Bufo_spinulosus_433)\n,(Bufo_amboroensis_TJ32,(Bufo_arenarum_567,(Bufo_marinus_523\n,Bufo_paracnemis_564))))))))))))))))))))))))))))))))))))));\n(Latimeria_chalumnae_1114,(((Didelphis_marsupialis_1092\n,Gazella_thomsoni_1093),((Alligator_sinensis_1090,Iguana_iguana_1001)\n,(Chelydra_serpentina_1091,Pelomedusa_subrufa_1051))),(((Epicrionops_sp_917\n,Rhinatrema_bivittatum_TJ29),((Ichthyophis_sp_TJ102\n,(Ichthyophis_peninsularis_878,Uraeotyphlus_narayani_882))\n,((Boulengerula_uluguruensis_879,Herpele_squalostoma_TJ122)\n,((Caecilia_tentaculata_TJ52,Typhlonectes_natans_877)\n,((Crotaphatrema_tchabalmbaboensis_TJ118,Scolecomorphus_vittatus_TJ104)\n,((Geotrypetes_seraphini_TJ103,(Dermophis_oaxacae_TJ99\n,Schistometopum_gregorii_881)),(Gegeneophis_ramaswamii\n,(Hypogeophis_rostratus_918,Siphonops_hardyi_880))))))))\n,((((Batrachuperus_pinchoni_TJ105,Ranodon_sibiricus)\n,(Cryptobranchus_alleganiensis_1050,(Andrias_davidianus\n,Andrias_japonicus_1059))),((((Necturus_alabamensis_938\n,Necturus_maculosus_TJ6),(Pseudobranchus_striatus_969,(Siren_intermedia\n,Siren_lacertina_968))),(((Dicamptodon_aterrimus_909\n,Dicamptodon_tenebrosus_1048),(Ambystoma_cingulatum_970\n,(Ambystoma_mexicanum_996,Ambystoma_tigrinum_TJ53)))\n,(Salamandra_salamandra_TJ88,((Pleurodeles_waltl_TJ91\n,Tylototriton_shanjing_TJ4),((Notophthalmus_viridiscens_TJ7,Taricha_sp_TJ90)\n,((Pachytriton_brevipes_TJ92,Paramesotriton_sp_TJ76),(Neurergus_crocatus\n,(Euproctus_asper,Triturus_sp_TJ89)))))))),(Rhyacotriton_cascadae_900\n,(Amphiuma_tridactylum_910,((Plethodon_dunni_1049,((Ensatina_eschscholtzii\n,Plethodon_jordani_915),(Aneides_hardii,((Desmognathus_quadramaculatus_1040\n,Desmognathus_wrighti),(Phaeognathus_hubrichti\n,(Hydromantes_platycephalus_1013,Speleomantes_italicus))))))\n,((Batrachoseps_attenuatus,Batrachoseps_wrightorum)\n,(Hemidactylum_scutatum_911,((Eurycea_wilderae_1041\n,Gyrinophilus_porphyriticus_1042),((Nototriton_abscondens,(Oedipina_uniformis\n,(Cryptotriton_alvarezdeltoroi,Dendrotriton_rabbi))),(Thorius_sp_TJ100\n,((Bolitoglossa_rufescens_TJ101,Parvimolge_townsendi),(Ixalotriton_niger\n,(Lineatriton_lineolus,Pseudoeurycea_conanti_TJ98)))))))))))))\n,((Ascaphus_truei_907,(Leiopelma_archeyi_998,Leiopelma_hochstetteri_999))\n,((Rhinophrynus_dorsalis_899,(Hymenochirus_boettgeri,((Pipa_carvalhoi_1038\n,Pipa_pipa_457),(Silurana_tropicalis_TJ128,(Xenopus_gilli_TJ9,Xenopus_laevis)\n)))),(((Alytes_obstetricans_902,(Discoglossus_galganoi_1029\n,Discoglossus_pictus_TJ83)),(Bombina_microdeladigitora_TJ54\n,(Bombina_orientalis_TJ80,(Bombina_bombina_1035,Bombina_variegata_1034))))\n,(((Pelodytes_puntatus_901,(Spea_hammondii_966,(Scaphiopus_couchii_937\n,Scaphiopus_holbrooki_943))),((Pelobates_cultripes,Pelobates_fuscus_903)\n,((Leptolalax_pelodytoides_TJ25,(Leptobrachium_chapaense_450\n,Leptobrachium_hasselti_1022)),(Brachytarsophrys_feae,((Xenophrys_major\n,Xenophrys_major_TJ19),(Megophrys_nasuta_TJ107,(Ophryophryne_microstoma_TJ36\n,Ophryophryne_poilani_TJ21))))))),((Heleophryne_purcelli_633\n,Heleophryne_regis_906),((((Kalophrynus_pleurostigma_933\n,(Synapturanus_mirandaribeiroi_530,((Micryletta_inornata\n,Phrynomantis_bifasciatus_941),((((Hoplophryne_rogersi_TJ68\n,Ramanella_obscura),((Anodonthyla_montana,Platypelis_sp_TJ58)\n,(Plethodontohyla_sp_TJ56,Stumpffia_sp_TJ59))),((Ctenophryne_geayei_TJ27\n,Nelsonophryne_aequatorialis),(Dasypops_schirchi_888\n,(Hamptophryne_boliviana_TJ86,(Elachistocleis_ovalis_TJ51\n,(Dermatonotus_muelleri_1185,(Gastrophryne_elegans_TJ74\n,Gastrophryne_olivacea_1053))))))),((Scaphiophryne_marmorata_TJ57\n,(Kaloula_pulchra_TJ41,(Chaperina_fusca_932,(Calluella_guttulata_931\n,(Microhyla_heymonsi_TJ26,Microhyla_sp_TJ70))))),(Dyscophus_guineti_TJ82\n,((Choerophryne_sp_991,Cophixalus_sphagnicola_990),((Genyophryne_thomsoni_993\n,(Copiula_sp_992,Sphenophryne_sp_989)),(Liophryne_rhododactyla_983\n,(Aphantophryne_pansa_980,(Callulops_slateri,Oreophryne_brachypus_979))))))))\n))),((Hemisus_marmoratus_TJ78,(Breviceps_mossambicus_942\n,(Probreviceps_macrodactylus_TJ69,(Callulina_kisiwamsitu_TJ77\n,Callulina_kreffti)))),(((Acanthixalus_spinosus,(Kassina_senegalensis_TJ85\n,Phlyctimantis_leonardi_TJ119)),(Opisthothylax_immaculatus_962\n,(((Afrixalus_fornasinii_TJ44,Afrixalus_pygmaeus_1019)\n,(Tachycnemis_seychellensis_TJ95,(Heterixalus_sp_TJ93,Heterixalus_tricolor)))\n,(Cryptothylax_gresshoffi_959,((Alexteroon_obstetricans_960\n,Alexteroon_obstetricans_TJ109),(Hyperolius_tuberilinguis_TJ43\n,(Hyperolius_alticola_1011,(Hyperolius_punticulatus_TJ35\n,Nesionixalus_thomensis_1017)))))))),((Leptopelis_argenteus_1012\n,(Leptopelis_bocagei_TJ67,(Leptopelis_sp_950,Leptopelis_vermiculatus_1026)))\n,((Leptodactylodon_bicolor_TJ129,(Nyctibates_corrugatus_TJ126\n,(Astylosternus_schiotzi_TJ116,Trichobatrachus_robustus_TJ111)))\n,(Scotobleps_gabonicus_TJ130,((Cardioglossa_gratiosa_964\n,Cardioglossa_leucomystax_845),((Schoutedenella_sylvatica_844\n,Schoutedenella_taeniata_1018),((Arthroleptis_tanneri_TJ75\n,Arthroleptis_variabilis_847),(Schoutedenella_schubotzi_1021\n,Schoutedenella_xenodactyloides_TJ79))))))))))\n,((Ptychadena_mascareniensis_181,(Ptychadena_anchietae\n,Ptychadena_cooperi_588)),((Ingerana_baluensis_929,(Discodeles_guppyi_984\n,(Ceratobatrachus_guentheri_982,(Batrachylodes_vertebralis_994\n,(Platymantis_pelewensis_896,Platymantis_weberi_981))))),((Micrixalus_fuscus\n,Micrixalus_kottigeharensis),((((Phrynobatrachus_dendrobates_1015\n,Phrynodon_sandersoni_848),((Dimorphognathus_africanus_963\n,(Phrynobatrachus_auritus_849,Phrynobatrachus_natalensis_TJ61))\n,(Phrynobatrachus_calcaratus_1024,(Phrynobatrachus_dispar_1009\n,Phrynobatrachus_mababiensis_TJ72)))),(((Conraua_goliath_919\n,Conraua_robusta_TJ113),((Indirana_sp1_FB2000a,Indirana_sp2_FB2000b)\n,(Arthroleptides_sp_TJ62,(Petropedetes_palmipes_841,(Petropedetes_newtoni_965\n,(Petropedetes_cameronensis_843,Petropedetes_parkeri))))))\n,((Pyxicephalus_edulis_944,(Aubria_subsigillata_961\n,Aubria_subsigillata_TJ117)),(Tomopterna_delalandii_TJ5\n,((Arthroleptella_bicolor_591,Natalobatrachus_bonebergi)\n,((Afrana_fuscigula_590,(Afrana_angolensis_1014,Amietia_vertebralis_TJ45))\n,(Strongylopus_grayii_589,(Anhydrophryne_rattrayi,Cacosternum_platys_1045))))\n)))),(((Micrixalus_borealis_1020,(Occidozyga_baluensis_930\n,(Occidozyga_laevis_TJ12,Occidozyga_lima_1010))),((Limnonectes_kuhlii_TJ14\n,(Limnonectes_grunniens_986,(Limnonectes_blythi_TJ22,(Taylorana_limborgi\n,(Limnonectes_acanthi,(Limnonectes_heinrichi,Limnonectes_visayanus))))))\n,((Paa_verrucospinosa_TJ23,Quasipaa_exilispinosa_1030),(Nanorana_pleskei\n,((Fejervarya_cancrivorus,Fejervarya_limnocharis_TJ15)\n,((Sphaerotheca_breviceps_893,Sphaerotheca_pluvialis)\n,((Fejervarya_kirtisinghei,Fejervarya_syhadrensis),(Nannophrys_ceylonensis\n,(Euphlyctis_cyanophlyctis,(Hoplobatrachus_occipitalis_513\n,Hoplobatrachus_rugulosus_928)))))))))),((((Boophis_albilabris_185\n,Boophis_tephraeomystax_182),((Aglyptodactylus_madagascariensis_505\n,Laliostoma_labrosum_508),((Mantella_aurantiaca_238,Mantella_nigricans_204)\n,(Mantidactylus_cf_femoralis_187,Mantidactylus_peraccae_272))))\n,(Buergeria_japonica_502,(Philautus_gracilipes_446\n,((Chirixalus_eiffingeri_912,Chirixalus_idiooticus_500),(((Nyctixalus_905\n,Nyctixalus_pictus_920),(Philautus_rhododiscus_TJ37,Theloderma_corticale_445)\n),((Rhacophorus_annamensis_441,(Rhacophorus_bipunctatus_440\n,(Rhacophorus_calcaneus_TJ24,Rhacophorus_orlovi_443))),((Polypedates_cruciger\n,Polypedates_leucomystax_442),(Chirixalus_vittatus_921,(Chirixalus_doriae_922\n,Chiromantis_xerampelina_TJ42))))))))),((Lankanectes_corrugatus\n,(Nyctibatrachus_cf_aliciae,Nyctibatrachus_major)),(Staurois_tuberlinguis_927\n,((Sylvirana_guentheri_1052,(Hylarana_erythraea_925\n,Hylarana_taipehensis_TJ40)),(((Chalcorana_chalconota_926\n,(Amnirana_albilabris_TJ131,Amnirana_galamensis_512))\n,((Sylvirana_maosonensis_TJ18,Sylvirana_nigrovittata_TJ16)\n,(Sylvirana_temporalis,(Papurana_daemeli_985,Tylerana_arfaki_987))))\n,((Clinotarsus_curtipes,Meristogenys_orphnocnemis_934),(Glandirana_minima\n,((Amolops_hongkongensis,(Pelophylax_nigromaculata_924,Pelophylax_ridibunda))\n,(((Nidirana_adenopleura_908,Nidirana_chapaensis_TJ13)\n,((Amolops_chapaensis_TJ17,Odorrana_grahami_1025),(Huia_nasica_TJ11\n,Odorrana_livida_TJ38))),(((Amerana_mucosa_976,Aurorana_aurora_975)\n,(Pseudorana_johnsi_997,(Rana_japonica_923,(Pseudoamalops_sauteri_914\n,Rana_temporaria_916)))),((Aquarana_grylio_972,(Aquarana_heckscheri_977\n,(Aquarana_catesbeiana_1044,Aquarana_clamitans_971))),(Rana_sylvatica_TJ33\n,((Lithobates_palmipes_TJ28,(Sierrana_maculata_1076\n,Trypheropsis_warszewitschii_1043)),(Pantherana_capito_973\n,((Pantherana_chiricahuensis_1055,Pantherana_pipiens_913)\n,(Pantherana_berlandieri,(Pantherana_forreri_895\n,Pantherana_yavapaiensis_1057))))))))))))))))))))))),(((Nasikabatrachidae_sp\n,Nasikabatrachus_sahyadrensis),(Nesomantis_thomasseti_TJ96\n,Sooglossus_sechellensis_TJ94)),(((Caudiverbera_caudiverbera_TJ87\n,Telmatobufo_venustus_1131),((Kyarranus_sphagnicolus_1084\n,(Adelotus_brevis_1073,(((Neobatrachus_pictus_1070,Neobatrachus_sudelli_673)\n,(Notaden_melanoscaphus_1068,(Lechriodus_fletcheri_1065\n,Limnodynastes_ornatus_1064))),(Heleioporus_australiacus_1079\n,(Limnodynastes_dumerilli_1067,((Limnodynastes_depressus_1080\n,Limnodynastes_peronii_1032),(Limnodynastes_salmini\n,Megistolotis_lignarius_1069))))))),((Mixophyes_carbinensis_1086\n,Rheobatrachus_silus_1061),(Taudactylus_acutirostris_1062\n,(((Bryobatrachus_nimbus_1074,Crinia_signifera_978),(Paracrinia_haswelli_1077\n,(Assa_darlingtoni_1066,Geocrinia_victoriana_1072)))\n,((Spicospina_flammocaerulea_1075,Uperoleia_laevigata_1003)\n,((Pseudophryne_bibroni_677,Pseudophryne_coriacea_1082)\n,(Myobatachus_gouldii_1081,(Arenophryne_sp_1155,Metacrinia_nichollsi_1071))))\n))))),(Hemiphractus_helioi_467,((((Eleutherodactylus_binotatus_884\n,Ischnocnema_sp_521),(Barycholos_ternetzi_887,(Brachycephalus_ephippium_883\n,Eleutherodactylus_juipoca_886))),((Craugastor_pluvicanorus_TJ31\n,(Euhyas_planirostris_898,(Syrrhophus_marnockii_894,Syrrhophus_nitidus_1087))\n),((Phrynopus_sp_KU_202652,Phrynopus_sp_TJ30),(Craugastor_bufoniformis_954\n,((Craugastor_alfredi_1089,Craugastor_augusti_1056),(Craugastor_rhodopis_1088\n,(Craugastor_punctariolus_957,Craugastor_ranoides_897)))))))\n,((Cryptobatrachus_sp,Stefania_evansi_417),((Flectonotus_sp_690\n,(Gastrotheca_cf_marsupiata_317,Gastrotheca_fissipes_825))\n,(((((Agalychnis_calcarifer_1006,Phyllomedusa_vaillanti_103)\n,(Agalychnis_callidryas_TJ71,Phasmahyla_guttata_687)),((Litoria_meiriana_675\n,(Litoria_freycineti_672,Litoria_inermis_995)),(Nyctimistes_pulchra_676\n,((Litoria_nannotis_1000,Nyctimystes_dayi_1002),((Cyclorana_australis_674\n,Litoria_aurea_543),(Litoria_genimaculata_1004,Litoria_lesueurii_988))))))\n,(((Sphaenorhynchus_lacteus_138,(Scinax_garbei_90,Scinax_ruber_16))\n,((Hyloscirtus_armata_318,Hyloscirtus_palmeri_504),(Hypsiboas_granosus_416\n,((Aplastodiscus_perviridis_4,Hypsiboas_albomarginata_140)\n,(Hypsiboas_boans_486,Hypsiboas_multifasciata_102)))))\n,(((Scarthyla_goinorum_86,(Lysapsus_laevis_629,Pseudis_paradoxa_704))\n,(Dendropsophus_minutus_35,(Dendropsophus_marmoratus_468\n,(Dendropsophus_nana_172,Dendropsophus_parviceps_80))))\n,((Phyllodytes_luteolus_823,((Osteocephalus_cf_taurinus_410\n,Osteopilus_septentrionalis_139),(Argenteohyla_siemersi_pederseni_292\n,(Trachycephalus_jordani_540,Trachycephalus_venulosus_94))))\n,((Ecnomiohyla_miliaria_639,(Duellmanohyla_rufioculis_211\n,Ptychohyla_leonhardschultzei_796)),(Charadrahyla_nephila_551\n,(((Exerodonta_chimalapa_549,Plectrohyla_guatemalensis_802)\n,(Acris_crepitans_604,(Pseudacris_crucifer_638,Pseudacris_triseriata_833)))\n,((Hyla_arborea_871,Isthmohyla_rivularis_210),((Hyla_cinerea_207\n,Tlalocohyla_picta_658),(Smilisca_phaeota_459,(Anotheca_spinosa_552\n,Triprion_petasatus_458))))))))))),(((Allophryne_ruthveni_837\n,(Hyalinobatrachium_fleischmanni_TJ97,(Centrolene_prosoblepon_827\n,(Centrolene_geckoideum,Cochranella_bejaranoi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Vallin", + "alternate": [ + "Vallin, G." + ], + "firstname": "G.", + "lastname": "Vallin" + }, + { + "name": "M. Laurin", + "alternate": [ + "Laurin, M." + ], + "firstname": "M.", + "lastname": "Laurin" + } + ], + "editors": [], + "series_editors": [], + "figure": "6", + "identifier": [ + { + "type": "doi", + "id": "10.1671/5.1" + } + ], + "link": [], + "journal": { + "name": "Journal of Vertebrate Paleontology", + "volume": "24", + "identifier": [] + } + } + }, + { + "phylogenyCitation": { + "type": "article", + "title": "Initial diversification of living amphibians predated the breakup of Pangaea.", + "year": 2005, + "authors": [ + { + "name": "D. San Mauro", + "alternate": [ + "San Mauro, D." + ], + "firstname": "D.", + "lastname": "San Mauro" + }, + { + "name": "M. Vences", + "alternate": [ + "Vences, M." + ], + "firstname": "M.", + "lastname": "Vences" + }, + { + "name": "M. 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Plieninger", + "alternate": [ + "Plieninger, F." + ], + "firstname": "F.", + "lastname": "Plieninger" + } + ], + "editors": [], + "series_editors": [], + "publisher": "Palaeontographica", + "pages": "65-90", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The clade characterized by the apomorphy elongate wing metacarpal that is at least 80 percent as long as the humerus (at adult stage), as inherited by Pterodactylus antiquus (Soemmerring 1812).", + "internalSpecifiers": [], + "externalSpecifiers": [] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/newick-problems/CLADO_0000270.json.txt b/phyx/phylonym/newick-problems/CLADO_0000270.json.txt new file mode 100644 index 0000000..920741b --- /dev/null +++ b/phyx/phylonym/newick-problems/CLADO_0000270.json.txt @@ -0,0 +1,59 @@ +{ + "@context": "http://www.phyloref.org/phyx.js/context/v0.2.0/phyx.json", + "phylogenies": [ + { + "primaryPhylogenyCitation": { + "type": "article", + "title": "Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets.", + "year": 2006, + "authors": [ + { + "name": "T. L. Fulton", + "alternate": [ + "Fulton, T. L." + ], + "firstname": "T.", + "lastname": "Fulton", + "middlename": "L." + }, + { + "name": "C. Strobeck", + "alternate": [ + "Strobeck, C." + ], + "firstname": "C.", + "lastname": "Strobeck" + } + ], + "editors": [], + "series_editors": [], + "figure": "2", + "identifier": [ + { + "type": "doi", + "id": "10.1016/j.ympev.2006.05.025" + } + ], + "link": [], + "journal": { + "name": "Mol. Phylogenet. Evol.", + "volume": "41", + "identifier": [] + } + }, + "newick": "(((((((((Brown_bear, Polar_bear), (American_black_bear, Asiatic_black_bear)),\nSloth_bear), Sun_bear), Spectacled_bear), Giant_panda), \n\n((((((((Raccoon, Crab-eating_raccoon), Ringtail), \n(White-nosed_coati, Coati)), Kinkajou), \n\n((((((((((Sea_otter, Spotted_necked_otter), \n((African_clawless_otter, Oriental_small-clawed_otter), Eurasian_otter)), \n\n(N.A._river_otter, (Marine_otter, Neotropical_otter))), \nGiant_otter),\n(Grison, Zorilla)),\n\n((American_mink, Long-tailed_weasel), (Ermine, \n((((Ferret, European_polecat), Siberian_weasel, Steppe_polecat, Japanese_weasel),\nEuropean_mink), \n(Least_weasel, Mountain_weasel))))),\n\nChinese_ferret_badger), \n\n(Fisher, \n(((((American_marten, Pine_marten), Sable, Beech_marten, Japanese_marten), \nWolverine), Yellow-throated_marten), Tayra))),\n\n((European_badger, Japanese_badger), Hog-nosed_badger)), \n\nAmerican_badger)), \n\nRed_panda), \n\n((Striped_skunk, Western_spotted_skunk), Hog-nosed_skunk)),\n\n(\n((((South_American_fur_seal, New_Zealand_fur_seal), \n(South_American_sea_lion, Antarctic_fur_seal)), Steller's_sea_lion),\nWalrus), \n(\n((((Hooded_seal, (Grey_seal, Caspian_seal)), \n(Harbor_seal, Spotted_seal)), \nHarp_seal), Bearded_seal), \n\n(((((Leopard_seal, Weddell_seal), Crabeater_seal), Ross_seal), \nNorthern_elephant_seal), (Hawaiian_monk_seal, Mediterranean_monk_seal)))))),\n\n((Dog, Wolf), (Arctic_fox, Swift_fox))),\n\n(Cat, ((Lynx_Bobcat), (Cougar, (Siberian_tiger, African_lion)))))\n\n\n" + } + ], + "phylorefs": [ + { + "regnumId": 270, + "label": "Pan-Pinnipedia", + "dwc:scientificNameAuthorship": "Wolsan, M., Wyss, A. 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Evol.", + "volume": "41", + "identifier": [] + } + }, + "newick": "(((((((((Brown_bear, Polar_bear), (American_black_bear, Asiatic_black_bear)),\nSloth_bear), Sun_bear), Spectacled_bear), Giant_panda), \n\n((((((((Raccoon, Crab-eating_raccoon), Ringtail), \n(White-nosed_coati, Coati)), Kinkajou), \n\n((((((((((Sea_otter, Spotted_necked_otter), \n((African_clawless_otter, Oriental_small-clawed_otter), Eurasian_otter)), \n\n(N.A._river_otter, (Marine_otter, Neotropical_otter))), \nGiant_otter),\n(Grison, Zorilla)),\n\n((American_mink, Long-tailed_weasel), (Ermine, \n((((Ferret, European_polecat), Siberian_weasel, Steppe_polecat, Japanese_weasel),\nEuropean_mink), \n(Least_weasel, Mountain_weasel))))),\n\nChinese_ferret_badger), \n\n(Fisher, \n(((((American_marten, Pine_marten), Sable, Beech_marten, Japanese_marten), \nWolverine), Yellow-throated_marten), Tayra))),\n\n((European_badger, Japanese_badger), Hog-nosed_badger)), \n\nAmerican_badger)), \n\nRed_panda), \n\n((Striped_skunk, Western_spotted_skunk), Hog-nosed_skunk)),\n\n(\n((((South_American_fur_seal, New_Zealand_fur_seal), \n(South_American_sea_lion, Antarctic_fur_seal)), Steller's_sea_lion),\nWalrus), \n(\n((((Hooded_seal, (Grey_seal, Caspian_seal)), \n(Harbor_seal, Spotted_seal)), \nHarp_seal), Bearded_seal), \n\n(((((Leopard_seal, Weddell_seal), Crabeater_seal), Ross_seal), \nNorthern_elephant_seal), (Hawaiian_monk_seal, Mediterranean_monk_seal)))))),\n\n((Dog, Wolf), (Arctic_fox, Swift_fox))),\n\n(Cat, ((Lynx_Bobcat), (Cougar, (Siberian_tiger, African_lion)))))\n\n\n" + } + ], + "phylorefs": [ + { + "regnumId": 271, + "label": "Pinnipedia", + "dwc:scientificNameAuthorship": "Wolsan, M., Wyss, A. 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J. Peterson", + "alternate": [ + "Peterson, K. J." + ], + "firstname": "K.", + "lastname": "Peterson", + "middlename": "J." + }, + { + "name": "D. J. Eernisse", + "alternate": [ + "Eernisse, D. J." + ], + "firstname": "D.", + "lastname": "Eernisse", + "middlename": "J." + } + ], + "editors": [], + "series_editors": [], + "figure": "2 and 3", + "identifier": [ + { + "type": "doi", + "id": "10.1046/j.1525-142x.2001.003003170" + } + ], + "link": [], + "journal": { + "name": "Evolution and Development", + "volume": "3", + "identifier": [] + } + } + }, + { + "phylogenyCitation": { + "type": "article", + "title": "The new view of animal phylogeny.", + "year": 2004, + "authors": [ + { + "name": "K. M. Halanych", + "alternate": [ + "Halanych, K. M." + ], + "firstname": "K.", + "lastname": "Halanych", + "middlename": "M." + } + ], + "editors": [], + "series_editors": [], + "figure": "2", + "identifier": [ + { + "type": "doi", + "id": "10.1146/annurev.ecolsys.35.112202.130124" + } + ], + "link": [], + "journal": { + "name": "Annual Review of Ecology, Evolution, and Systematics", + "volume": "35", + "identifier": [] + } + } + }, + { + "phylogenyCitation": { + "type": "article", + "title": "Assessing the root of bilaterian animals with scalable phylogenomic methods.", + "year": 2009, + "authors": [ + { + "name": "A. Hejnol", + "alternate": [ + "Hejnol, A." + ], + "firstname": "A.", + "lastname": "Hejnol" + }, + { + "name": "M. Obst", + "alternate": [ + "Obst, M." + ], + "firstname": "M.", + "lastname": "Obst" + }, + { + "name": "A. Stamatakis", + "alternate": [ + "Stamatakis, A." + ], + "firstname": "A.", + "lastname": "Stamatakis" + }, + { + "name": "M. Ott", + "alternate": [ + "Ott, M." + ], + "firstname": "M.", + "lastname": "Ott" + }, + { + "name": "G. W. Rouse", + "alternate": [ + "Rouse, G. W." + ], + "firstname": "G.", + "lastname": "Rouse", + "middlename": "W." + }, + { + "name": "G. D. Edgecombe", + "alternate": [ + "Edgecombe, G. D." + ], + "firstname": "G.", + "lastname": "Edgecombe", + "middlename": "D." + }, + { + "name": "P. Martinez", + "alternate": [ + "Martinez, P." + ], + "firstname": "P.", + "lastname": "Martinez" + }, + { + "name": "J. Baguna", + "alternate": [ + "Baguna, J." + ], + "firstname": "J.", + "lastname": "Baguna" + }, + { + "name": "X. Bailly", + "alternate": [ + "Bailly, X." + ], + "firstname": "X.", + "lastname": "Bailly" + }, + { + "name": "U. Jondelius", + "alternate": [ + "Jondelius, U." + ], + "firstname": "U.", + "lastname": "Jondelius" + }, + { + "name": "M. Wiens", + "alternate": [ + "Wiens, M." + ], + "firstname": "M.", + "lastname": "Wiens" + }, + { + "name": "W. E. G. Muller", + "alternate": [ + "Muller, W. E. G." + ], + "firstname": "W. E.", + "lastname": "Muller", + "middlename": "G." + }, + { + "name": "E. Seaver", + "alternate": [ + "Seaver, E." + ], + "firstname": "E.", + "lastname": "Seaver" + }, + { + "name": "W. C. Wheeler", + "alternate": [ + "Wheeler, W. C." + ], + "firstname": "W.", + "lastname": "Wheeler", + "middlename": "C." + }, + { + "name": "M. Q. Martindale", + "alternate": [ + "Martindale, M. Q." + ], + "firstname": "M.", + "lastname": "Martindale", + "middlename": "Q." + }, + { + "name": "G. Giribet", + "alternate": [ + "Giribet, G." + ], + "firstname": "G.", + "lastname": "Giribet" + }, + { + "name": "C. W. Dunn", + "alternate": [ + "Dunn, C. W." + ], + "firstname": "C.", + "lastname": "Dunn", + "middlename": "W." + } + ], + "editors": [], + "series_editors": [], + "figure": "2", + "identifier": [ + { + "type": "doi", + "id": "10.1098/rspb.2009.0896" + } + ], + "link": [], + "journal": { + "name": "Proceedings of the Royal Society", + "volume": "276", + "identifier": [] + } + } + }, + { + "phylogenyCitation": { + "type": "article", + "title": "The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution.", + "year": 2013, + "authors": [ + { + "name": "J. F. Ryan", + "alternate": [ + "Ryan, J. F." + ], + "firstname": "J.", + "lastname": "Ryan", + "middlename": "F." + }, + { + "name": "K. Pang", + "alternate": [ + "Pang, K." + ], + "firstname": "K.", + "lastname": "Pang" + }, + { + "name": "C. E. Schnitzler", + "alternate": [ + "Schnitzler, C. E." + ], + "firstname": "C.", + "lastname": "Schnitzler", + "middlename": "E." + }, + { + "name": "A. D. Nguyen", + "alternate": [ + "Nguyen, A. D." + ], + "firstname": "A.", + "lastname": "Nguyen", + "middlename": "D." + }, + { + "name": "R. T. Moreland", + "alternate": [ + "Moreland, R. T." + ], + "firstname": "R.", + "lastname": "Moreland", + "middlename": "T." + }, + { + "name": "D. K. Simmons", + "alternate": [ + "Simmons, D. K." + ], + "firstname": "D.", + "lastname": "Simmons", + "middlename": "K." + }, + { + "name": "B. J. Koch", + "alternate": [ + "Koch, B. J." + ], + "firstname": "B.", + "lastname": "Koch", + "middlename": "J." + }, + { + "name": "W. R. Francis", + "alternate": [ + "Francis, W. R." + ], + "firstname": "W.", + "lastname": "Francis", + "middlename": "R." + }, + { + "name": "P. Havlak", + "alternate": [ + "Havlak, P." + ], + "firstname": "P.", + "lastname": "Havlak" + } + ], + "editors": [], + "series_editors": [], + "figure": "3", + "identifier": [], + "link": [], + "journal": { + "name": "Science", + "volume": "342", + "identifier": [] + } + } + }, + { + "phylogenyCitation": { + "type": "article", + "title": "Error, signal, and the placement of Ctenophora sister to all other animals.", + "year": 2015, + "authors": [ + { + "name": "N. V. Whelan", + "alternate": [ + "Whelan, N. V." + ], + "firstname": "N.", + "lastname": "Whelan", + "middlename": "V." + }, + { + "name": "K. M. Kocot", + "alternate": [ + "Kocot, K. M." + ], + "firstname": "K.", + "lastname": "Kocot", + "middlename": "M." + }, + { + "name": "L. L. Moroz", + "alternate": [ + "Moroz, L. L." + ], + "firstname": "L.", + "lastname": "Moroz", + "middlename": "L." + }, + { + "name": "K. M. Halanych", + "alternate": [ + "Halanych, K. M." + ], + "firstname": "K.", + "lastname": "Halanych", + "middlename": "M." + } + ], + "editors": [], + "series_editors": [], + "figure": "3", + "identifier": [ + { + "type": "doi", + "id": "10.1073/pnas.1503453112" + } + ], + "link": [], + "journal": { + "name": "Proceedings of the National Academy of Science U. S. A.", + "volume": "112", + "identifier": [] + } + } + } + ], + "phylorefs": [ + { + "regnumId": 188, + "label": "Bilateria", + "dwc:scientificNameAuthorship": "Lake, J. A., Garey, J. R., Servin, J. A., Halanych, K. M.", + "dwc:namePublishedIn": [ + { + "type": "book", + "title": "Lehrbuch der Zoologie 1.", + "year": 1888, + "authors": [ + { + "name": "B. Hatschek", + "alternate": [ + "Hatschek, B." + ], + "firstname": "B.", + "lastname": "Hatschek" + } + ], + "editors": [], + "series_editors": [], + "publisher": "Gustav Fischer", + "city": "Jena", + "pages": "1-114", + "identifier": [], + "link": [] + } + ], + "obo:IAO_0000119": [], + "cladeDefinition": "The largest crown clade containing Strongylocentrotus purpuratus (Stimpson 1857) (Deuterostomia, Echinodermata), Drosophila melanogaster Meigen 1830 (Ecdysozoa, Arthropoda), Capitella teleta Blake, Grassle & Eckelbarger 2009 (Lophotrochozoa, Annelida), and Paratomella rubra Rieger & Ott 1971 (Acoelomorpha, Acoela), but not Hydra vulgaris Pallas 1766 (Cnidaria) and Pleurobrachia bachei A. Agassiz 1860 (Ctenophora).", + "internalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Strongylocentrotus purpuratus 1857", + "nameComplete": "Strongylocentrotus purpuratus" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Drosophila melanogaster 1830", + "nameComplete": "Drosophila melanogaster" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Capitella teleta 2009", + "nameComplete": "Capitella teleta" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Paratomella rubra 1971", + "nameComplete": "Paratomella rubra" + } + }, + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Pleurobrachia bachei 1860", + "nameComplete": "Pleurobrachia bachei" + } + } + ], + "externalSpecifiers": [ + { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", + "hasName": { + "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", + "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107", + "label": "Hydra vulgaris 1766", + "nameComplete": "Hydra vulgaris" + } + } + ] + } + ] +} \ No newline at end of file diff --git a/phyx/phylonym/scripts/phyx2owl.js b/phyx/phylonym/scripts/phyx2owl.js new file mode 100644 index 0000000..6610573 --- /dev/null +++ b/phyx/phylonym/scripts/phyx2owl.js @@ -0,0 +1,121 @@ +#!/usr/bin/env node + +const fs = require('fs'); +const path = require('path'); +const phyx = require('@phyloref/phyx'); + +/* + * An application for converting input Phyx files to OWL ontologies. + */ + +// Read command line arguments. +const argv = require('yargs') + .usage("$0 [files to convert into OWL ontologies]") + .describe('max-internal-specifiers', 'The maximum number of internal specifiers (phylorefs with more than this number will be ignored)') + .default('max-internal-specifiers', 8) + .describe('max-external-specifiers', 'The maximum number of external specifiers (phylorefs with more than this number will be ignored)') + .default('max-external-specifiers', 8) + .help() + .alias('h', 'help') + .argv + +const filenames = argv._; + +/* + * Get a list of all files in a directory. We will recurse into directories and choose files that meet the + * criteria in the function `check(filename) => boolean`. + */ +function getFilesInDir(dir, check = (filename => filename.toLowerCase().endsWith(".json"))) { + // console.debug(`Processing file: ${dir}`) + if (!fs.existsSync(dir)) return []; + + const lsync = fs.lstatSync(dir); + if (lsync.isFile()) { + if (!check(dir)) { + // console.log(`Skipping ${dir}.`) + return []; + } else { + return [dir]; + } + } else if (lsync.isDirectory()) { + const files = fs.readdirSync(dir); + return files.map(file => getFilesInDir(path.join(dir, file), check)) + .reduce((acc, curr) => acc.concat(curr), []) + .filter(filename => filename); + } else { + // console.debug(`${dir} is neither a file nor a directory; skipping.`); + return []; + } +} +const files = filenames.map(filename => getFilesInDir(filename)).reduce((acc, curr) => acc.concat(curr), []); +// console.debug(`Files to process: ${files.join(", ")}`); + +/* + * Convert the input file into the output filename. + * If no argOutputFilename is given, we generate one from the input + * filename: either by replacing '.json' with '.owl', or by concatenating + * '.owl' at the end. + */ +function convertFileToOWL(filename, argOutputFilename = "") { + // console.debug(`Starting with ${filename}.`); + let outputFilename; + if (argOutputFilename != "") { + outputFilename = argOutputFilename; + } else if (filename.toLowerCase().endsWith(".json")) { + outputFilename = filename.substring(0, filename.length - 5) + ".owl"; + } else { + outputFilename = filename + ".owl"; + } + + try { + // Parse the input file into JSON. + let phyxContent = JSON.parse(fs.readFileSync(filename)); + + // Remove any phylorefs that have too many specifiers. + const phylorefCount = (phyxContent.phylorefs || []).length; + filteredPhylorefs = (phyxContent.phylorefs || []).filter(phyloref => { + const wrappedPhyloref = new phyx.PhylorefWrapper(phyloref); + const internalSpecifiersCount = wrappedPhyloref.internalSpecifiers.length; + const externalSpecifiersCount = wrappedPhyloref.externalSpecifiers.length; + if (internalSpecifiersCount > argv.maxInternalSpecifiers) { + console.warn(`Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${internalSpecifiersCount} internal specifiers.`); + return false; + } else if (externalSpecifiersCount > argv.maxExternalSpecifiers) { + console.warn(`Phyloreference ${wrappedPhyloref.label} was skipped, since it has ${externalSpecifiersCount} external specifiers.`); + return false; + } + return true; + }); + phyxContent.phylorefs = filteredPhylorefs; + + const wrappedPhyx = new phyx.PhyxWrapper(phyxContent); + const owlOntology = wrappedPhyx.asJSONLD(); + const owlOntologyStr = JSON.stringify(owlOntology, null, 2); + fs.writeFileSync( + outputFilename, + owlOntologyStr + ); + + if (filteredPhylorefs.length == 0) { + console.warn(`No phyloreferences in ${filename} were converted to ${outputFilename}, as they were all filtered out.`); + return false; + } else if (phylorefCount > filteredPhylorefs.length) { + console.warn(`Only ${filteredPhylorefs.length} out of ${phylorefCount} were converted from ${filename} to ${outputFilename}.`); + return true; + } else { + console.info(`Converted ${filename} to ${outputFilename}.`); + return true; + } + + return true; + } catch(e) { + console.error(`Could not convert ${filename} to ${outputFilename}: ${e}`); + } + return false; +} +const successes = files.map(file => convertFileToOWL(file)); +if(successes.every(x => x)) { + console.log(`${successes.length} files converted successfully.`); +} else { + console.log(`Errors occurred; ${successes.filter(x => x).length} files converted successfully, ${successes.filter(x => !x).length} files failed.`); +} diff --git a/phyx/phylonym/scripts/phyxfix.js b/phyx/phylonym/scripts/phyxfix.js new file mode 100644 index 0000000..d032141 --- /dev/null +++ b/phyx/phylonym/scripts/phyxfix.js @@ -0,0 +1,106 @@ +#!/usr/bin/env node + +const fs = require('fs'); +const path = require('path'); +const lodash = require('lodash'); + +/* + * An application for fixing Phyx files. + */ + +// Read command line arguments. +const argv = require('yargs') + .usage("$0 [source files]") + .describe('compare-to', 'A directory containing "fixed" Phyx files.') + .required('compare-to') + .help() + .alias('h', 'help') + .argv + +const filenames = argv._; + +function getFilesInDir(dir, check = (filename => filename.toLowerCase().endsWith(".json"))) { + // console.debug(`Processing file: ${dir}`) + if (!fs.existsSync(dir)) return []; + + const lsync = fs.lstatSync(dir); + if (lsync.isFile()) { + if (!check(dir)) { + // console.log(`Skipping ${dir}.`) + return []; + } else { + return [dir]; + } + } else if (lsync.isDirectory()) { + const files = fs.readdirSync(dir); + return files.map(file => getFilesInDir(path.join(dir, file), check)) + .reduce((acc, curr) => acc.concat(curr), []) + .filter(filename => filename); + } else { + // console.debug(`${dir} is neither a file nor a directory; skipping.`); + return []; + } +} +const files = filenames.map(filename => getFilesInDir(filename)).reduce((acc, curr) => acc.concat(curr), []); +// console.debug(`Files to process: ${files.join(", ")}`); + +function readJSON(filename) { + return JSON.parse(fs.readFileSync(filename)); +} + +function fixSpecifiers(phyloref, source, comparison) { + console.info(`For phyloref ${phyloref.label} (Regnum ID ${phyloref.regnumId})`); + if(source === undefined || comparison === undefined) return; + source.forEach((specifier, index) => { + if (!lodash.has(specifier, 'hasName')) return; + if (!lodash.has(comparison[index], 'hasName')) return; + + const sourceName = specifier.hasName.nameComplete; + const sourceLabel = specifier.hasName.label; + + const comparisonName = comparison[index].hasName.nameComplete; + const comparisonLabel = comparison[index].hasName.label; + + console.info(` - Comparing ${sourceLabel} with ${comparisonLabel}`); + + if (sourceName !== "" && sourceName === comparisonName) { + // Safe to replace old label with new label! + source[index].hasName.label = comparisonLabel; + } else { + console.warn(`Cannot fix ${sourceLabel}: ${sourceName} doesn't match ${comparisonName}`) + } + }); +} + +function fixJSON(source, comparison) { + source.phylorefs.forEach((phyloref, index) => { + const comparisonPhyloref = comparison.phylorefs[index]; + fixSpecifiers(phyloref, phyloref.internalSpecifiers, comparisonPhyloref.internalSpecifiers); + fixSpecifiers(phyloref, phyloref.externalSpecifiers, comparisonPhyloref.externalSpecifiers); + }); + + return source; +} + +files.forEach(file => { + // Is there a comparison? If not, no fixing is possible. + const filename = path.basename(file); + const comparisonFile = path.join(argv.compareTo, filename) + if (!fs.existsSync(comparisonFile)) { + console.warn(`Could not find a comparison for file ${filename} at ${comparisonFile}.`); + } else { + // console.info(`Comparing ${file} with ${comparisonFile}.`); + const content = readJSON(file); + const comparison = readJSON(comparisonFile); + const fixedJSON = fixJSON(content, comparison); + if (fixedJSON !== undefined) { + const fixedJSONString = JSON.stringify(fixedJSON, null, 4); + fs.writeFileSync( + file, + fixedJSONString + ); + } else { + console.info(`No corrections made to ${file}`); + } + } +}); diff --git a/regnum2phyx/regnum2phyx.js b/regnum2phyx/regnum2phyx.js index e9a7d3b..8e1e9cc 100644 --- a/regnum2phyx/regnum2phyx.js +++ b/regnum2phyx/regnum2phyx.js @@ -31,16 +31,17 @@ const { } = require('lodash'); // Helper functions. -function convertAuthorsIntoStrings(authors, lastNameFirst = true) { +function convertAuthorsIntoStrings(authors, lastNameStatus = 'first') { // Given a list of authors with first_name, middle_name and last_name properties, // return a list of author names with a single name. // - // We combine author names in two possible ways: - // If lastNameFirst is true: $last_name $first_name $middle_name - // If lastNameFirst is false: $first_name $middle_name $last_name + // We combine author names in three possible ways: + // If lastNameStatus is 'first': $last_name $first_name $middle_name + // If lastNameStatus is 'only': $last_name + // Any other value: $first_name $middle_name $last_name // The middle name will be ignored if it is blank or not present. - if (lastNameFirst) { + if (lastNameStatus === 'first') { // Use "last first middle". return authors.map(author => ( `${author.last_name || ''}, ${author.first_name || ''}${ @@ -49,6 +50,11 @@ function convertAuthorsIntoStrings(authors, lastNameFirst = true) { )).filter(name => name !== ''); } + if (lastNameStatus === 'only') { + // Use "last". + return authors.map(author => `${author.last_name || ''}`.trim()).filter(name => name !== ''); + } + // Use "first middle last". return authors.map(author => ( `${author.first_name || ''} ${ @@ -65,10 +71,10 @@ function convertAuthorsIntoBibJSON(authors) { .filter(author => author.last_name) .map(author => pickBy({ // lodash.pickBy will remove empty keys from the object. // We store the author name as first_name middle_name last_name - name: convertAuthorsIntoStrings([author], false).join(), + name: convertAuthorsIntoStrings([author], 'last').join(' and '), alternate: [ // We store an alternate author name as last_name, first_name middle_name. - convertAuthorsIntoStrings([author], true).join(), + convertAuthorsIntoStrings([author], 'first').join(' and '), ], firstname: (author.first_name || '').trim(), lastname: (author.last_name || '').trim(), @@ -183,6 +189,11 @@ const argv = yargs 'regnum-id', ], }) + .option('digits', { + describe: 'Number of digits to put into CLADO name', + type: 'number', + default: 7, + }) .option('filename-prefix', { describe: 'Choose the prefix for the filename being generated', string: true, @@ -232,7 +243,7 @@ dump.forEach((entry, index) => { const phylorefTemplate = pickBy({ regnumId: entry.id, label: phylorefLabel, - 'dwc:scientificNameAuthorship': (convertAuthorsIntoStrings(entry.authors)).join(', '), + 'dwc:scientificNameAuthorship': (convertAuthorsIntoStrings(entry.authors)).join(' and '), 'dwc:namePublishedIn': convertCitationsToBibJSON(entry.citations.preexisting), 'obo:IAO_0000119': // IAO:definition source (http://purl.obolibrary.org/obo/IAO_0000119) convertCitationsToBibJSON(entry.citations.definitional), @@ -265,7 +276,7 @@ dump.forEach((entry, index) => { // Set up specifier name, authorship and nomenclatural code. const specifierName = (specifier.specifier_name || '').trim(); - const specifierAuthors = (specifier.displayAuths || '').trim(); + const specifierAuthors = convertAuthorsIntoStrings(specifier.authors, 'only').join(' and '); const specifierCode = (specifier.specifier_code || '').trim(); let nomenCode = NAME_IN_UNKNOWN_CODE; @@ -319,7 +330,7 @@ dump.forEach((entry, index) => { }); // Write out Phyx file for this phyloreference. - const fileIndex = `${index + 1}`.padStart(6, '0'); + const fileIndex = `${index + 1}`.padStart(argv.digits, '0'); const filePrefix = argv.filenamePrefix || ''; let phyxFilename; if (argv.filenames === 'label') { @@ -327,7 +338,7 @@ dump.forEach((entry, index) => { phyxFilename = path.join(argv.outputDir, `${phylorefLabel}.json`); } else if (argv.filenames === 'regnum-id') { // Use the regnum id. - if (entry.id) phyxFilename = path.join(argv.outputDir, `CLADO_${(`${entry.id}`).padStart(6, '0')}.json`); + if (entry.id) phyxFilename = path.join(argv.outputDir, `CLADO_${(`${entry.id}`).padStart(argv.digits, '0')}.json`); else phyxFilename = path.join(argv.outputDir, `${filePrefix}${fileIndex}.json`); } else { // Default to just the number of the sequence. diff --git a/test/regnum2phyx/expected/Crocodylia/Crocodylia.json b/test/regnum2phyx/expected/Crocodylia/Crocodylia.json index f62b6d4..4f5f2f7 100644 --- a/test/regnum2phyx/expected/Crocodylia/Crocodylia.json +++ b/test/regnum2phyx/expected/Crocodylia/Crocodylia.json @@ -104,7 +104,7 @@ "@type": "http://rs.tdwg.org/ontology/voc/TaxonConcept#TaxonConcept", "hasName": { "@type": "http://rs.tdwg.org/ontology/voc/TaxonName#TaxonName", - "label": "Crocodylus niloticus Gmelin, 1768", + "label": "Crocodylus niloticus Laurenti, 1768", "nameComplete": "Crocodylus niloticus", "nomenclaturalCode": "http://purl.obolibrary.org/obo/NOMEN_0000107" } diff --git a/test/test_phyx.js b/test/test_phyx.js index 428db3d..57f5bb1 100644 --- a/test/test_phyx.js +++ b/test/test_phyx.js @@ -114,7 +114,27 @@ describe('Test Phyx files in repository', function () { return; } - console.log(`Loaded Phyx file ${filename}`); + it('has at least one Newick phylogeny', function () { + const phylogenies = json.phylogenies || []; + // assert.isAbove(phylogenies.length, 0, 'No phylogenies found in file'); + + const newicks = phylogenies + .map(ph => ph.newick || []) + .reduce((a, b) => a.concat(b), []) + .filter(nw => nw.trim() !== ''); + // assert.isAbove(newicks.length, 0, 'No Newick phylogenies found in file'); + if (newicks.length === 0) { + console.warn(`No Newick phylogenies found in file ${filename}.`); + } + + // assert.equal(newicks.length, 1, + // `Contains ${newicks.length} Newick phylogenies in ${phylogenies.length} phylogenies.`); + if (newicks.length > 1) { + console.warn(`Unexpectedly found ${newicks.length} Newick phylogenies in ${phylogenies.length} phylogenies in Phyx file ${filename}.`); + } + }); + + // console.log(`Loaded Phyx file ${filename}`); const skipFile = (json.phylorefs || []) .map(phyloref => new phyx.PhylorefWrapper(phyloref)) @@ -175,7 +195,7 @@ describe('Test Phyx files in repository', function () { // Eventually, we will parse the TAP results directly. const matches = /Testing complete:(\d+) successes, (\d+) failures, (\d+) failures marked TODO, (\d+) skipped./.exec(child.stderr); assert(matches !== null, `Test result line not found in STDERR <${child.stderr}>`); - console.log(`For ${filename}: ${matches}`); + // console.log(`For ${filename}: ${matches}`); // Test whether we have any failures. it('did not report any failures', function () {