data/orReferenceTree.R

In ms609/OReillyEtAl2016: Distance metrics for trees generated by O'Reilly et al. 2016

orReferenceTree <- ape::read.tree(text='(Osteolepiformes, (Panderichthyidae, ((Acanthostega, (Tulerpeton, Ichthyostega)), (((Archeria, Proterogyrinus), (Colosteidae, (Crassigyrinus, Baphetidae))), ((Dendrerpeton, ((Ecolsonia, Eryops), ((Doleserpeton, Amphibamus), (Apateon, Tersomius)))), ((Gephyrostegidae, (Kotlassia, (Seymouria, Ariekanerpeton))), ((Westlothiana, ((Solenodonsaurus, (Limnoscelis, Diadectes)), (Synapsida, (Captorhinidae, Procolophonidae)))), (((Adelogyrinidae, Microbrachis), (Utaherpeton, Nectridea)), (Aistopoda, ((Pantylus, Asaphestera), ((Cardiocephalus, Rhynchonkos), (Brachystelechidae, (Lysorophia, ((Eocaecilia, (Rhinatrematidae, (Ichthyophiidae, (Typhlonectidae, Caeciliidae)))), (((Karaurus, (Hynobiidae, Cryptobranchidae)), (Sirenidae, ((Proteidae, (Salamandridae, (Ambystomatidae, Dicamptodontidae))), (Rhyacotritonidae, (Amphiumidae, (Plethodontinae, (Bolitoglossinae, (Spelerpinae, Hemidactylinae)))))))), (Triadobatrachus, ((Leiopelmatidae, Ascaphidae), (((Discoglossidae, Bombinatoridae), (Pipidae, Rhinophrynidae)), ((Scaphiopodidae, (Pelodytidae, (Megophryidae, Pelobatidae))), ((Sooglossidae, Ranoidea), (Heleophrynidae, (Myobatrachidae, (Calyptocephallidae, Hyloidea)))))))))))))))))))))));')

#read.tree(text='(Osteolepiformes, (Panderichthyidae,
#  (
#    (Acanthostega, (Tulerpeton, Ichthyostega))
#    ,
#    (
#      ((Archeria, Proterogyrinus), (Colosteidae, (Crassigyrinus, Baphetidae)))
#      ,
#      (
#        (Dendrerpeton, ((Ecolsonia, Eryops), ((Doleserpeton, Amphibamus), (Apateon, Tersomius))))
#        ,
#        (
#          (Gephyrostegidae, (Kotlassia, (Seymouria, Ariekanerpeton)))
#          ,
#          (
#            (Westlothiana, ((Solenodonsaurus, (Limnoscelis, Diadectes)), (Synapsida, (Captorhinidae, Procolophonidae))))
#            ,
#            (
#              ((Adelogyrinidae, Microbrachis), (Utaherpeton, Nectridea))
#              ,
#              (Aistopoda,
#                ((Pantylus, Asaphestera),
#                  ((Cardiocephalus, Rhynchonkos),
#                    (Brachystelechidae,
#                      (Lysorophia,
#                        (
#                          (Eocaecilia, (Rhinatrematidae, (Ichthyophiidae, (Typhlonectidae, Caeciliidae))))
#                          ,
#                          (
#                            (
#                              (Karaurus, (Hynobiidae, Cryptobranchidae))
#                              ,
#                              (Sirenidae,
#                                (
#                                  (Proteidae, (Salamandridae, (Ambystomatidae, Dicamptodontidae)))
#                                  ,
#                                  (Rhyacotritonidae, (Amphiumidae, (Plethodontinae, (Bolitoglossinae, (Spelerpinae, Hemidactylinae)))))
#                                )
#                              )
#                            )
#                            ,
#                            (Triadobatrachus,
#                              (
#                                (Leiopelmatidae, Ascaphidae)
#                                ,
#                                (
#                                  ((Discoglossidae, Bombinatoridae), (Pipidae, Rhinophrynidae))
#                                  ,
#                                  (
#                                    (Scaphiopodidae, (Pelodytidae, (Megophryidae, Pelobatidae)))
#                                    ,
#                                    (
#                                      (Sooglossidae, Ranoidea)
#                                      ,
#                                      (Heleophrynidae, (Myobatrachidae, (Calyptocephallidae, Hyloidea)))
#                                    )
#                                  )
#                                )
#                              )
#                            )
#                          )
#                        )
#                      )
#                    )
#                  )
#                )
#              )
#            )
#          )
#        )
#      )
#    )
#  )
#));')