fix hit count to go with database change, tests pass with BLAST+ 2.2.25+

[bioperl-run.git] / t / data / tree_of_life

//START
(
 //EUBACTERIA
 (
  AQUIFEX*,
  (
   THERMOTOGA*,
   DEINOCOCCUS*,
   (
    (
     (
      //BACILLUS
      (
       BACILLUS
      ),
      //MYCOPLASMA
      (
       MYCOPLASMA_PNEUMONIAE,
       MYCOPLASMA_GENITALIUM
      )
     ),
     //ACTINOBACTERIA
     (
      MYCOBACTERIUM*
     )
    ),
    (
     SYNECHOCYSTIS*,
     (
      (
       //SPIROCHAETALES
       (
        //SPIROCHAETACEAE
        TREPONEMA*,
        BORRELIA*
       ),
       (
        //CHLAMYDIA
        CHLAMYDIA*
       )
      ),
      (
       (
        //ALPHA
        RICKETTSIA*
       ),
       (
        //GAMMA
        (
         //ESCHERICHIA
         ESCHERICHIA*,
         BUCHNERA*
        ),
        PSEUDOMONAS*,
        VIBRIO*,
        HAEMOPHILUS*,
        XYLELLA*
       ),
       (
        //BETA
        NEISSERIA*
       ),
       (
        //EPSILON
        HELICOBACTER*,
        CAMPYLOBACTER*
       )
      )
     )
    )
   )
  )
 ),  // END OF EUBACTERIA
 //ARCHEA+EUKARYA
 (      
  //ARCHEA
  (
   (
    DESULFUROCOCCUS,
    SULFOLOBUS
   ),
   (
    (
     //PYROCOCCUS
     (
      PYROCOCCUS*
     ),
     AEROPYRUM*
    ),
    (
     METHANOBACTERIUM*,
     (
      METHANOCOCCUS*,
      (
       ARCHAEOGLOBUS*,
       (
        THERMOPLASMA*1,
        HALOBACTERIUM*
       )
      )
     )
    )
   )
  ),  // END OF ARCHEA  
  //EUKARYA
  (
  //PROTISTA+PLANT  (DUBIOUS)
   (
    (
     GIARDIA,
     ENTAMOEBA
    ),
    //PLANTS
    (
     HUMULUS,
     ORYZA
    )
   ),  // END OF PROTISTA+ PLANTS
   //FUNGI+ANIMALS
   (
    //FUNGI
    (
     VERTICILLIUM,
     SACCHAROMYCES
    ), // END OF FUNGI
    //METAZOAN
    (
     //SPONGES
     EPHYDATIA*,
     HYDRA*,
     LYMNAEA*, //SNAIL
     //ARTHROPODA
     (
      (
       IXODES*,
       CALPODES*, 
       ORNITHODOROS
      )
      ,
      //INSECTA
      (       
       //Lepidoptera
       (  
        GALLERIA*,
        MANDUCA*,
        (
         // BOMBYCOIDEA
         (
          BOMBYX_MANDARINA,
          BOMBYX_MORI,
          HYALOPHORA*
         ),
         (
          ANTHERAEA_PERNYI,
          ANTHERAEA_YAMAMAI
         )
        )
       ),
       NILAPARVATA*,
       //DIPTERA
       (
        MUSCA,
        (
         (DROSOPHILA_MELANOGASTER,
          DROSOPHILA_SIMULANS),
         DROSOPHILA_VIRILIS,
         DROSOPHILA
        ),     
        //NEMATOCERA
        (
         //CULICOIDEA
         (
          AEDES*,
          CULEX*,
          ANOPHELES*
         ),
         //SCIAROIDEA
         (
          RHYNCHOSCIARA*,
          CHIRONOMUS*
         )
        )
       )
      ),
      TIGRIOPUS*,
      DAPHNIA*,
      PACIFASTACUS*
     ),
     //VERTEBRATE+CELEGANS
     (
      CAENORHABDITIS*,
      //DEUTEROSTOMA
      (
       //ECHINODERMS
       ( 
        //ELEUTHEROZOA
        (
         LYTECHINUS*,
         //ECHINIDAE
         (
          PARACENTROTUS*,
          PSAMMECHINUS*
         )
        ),
        //ASTEROZOA
        (
         PYCNOPODIA*,
         PISASTER*
        )
       ),
      //VERTEBRATES
      (
       //HYPEROARTIA
       (
        (PETROMYZON,LAMPREY)
       ),
       //GNATHOSTOMATA
       (
        SCYLIORHINUS,
        //BONYFISHES
        (
          //OSTARIOPHYSI
          (
           (CATFISH,ICTALURUS*),
           //CYPRIFORMES
           (
            MISGURNUS*,
            BARBATULA*,
            //CYPRINIDAE
            (
             CATLA*,             
             (ZEBRAFISH,DANIO*),
             // CARPS
             (      
              (COMMONCARP,CYPRINUS*),
              (GRASSCARP,CTENOPHARYNGODON*),
              LABEO*              
             ),
             (GOLDFISH,CARASSIUS*)
            ) 
           )
          ),
          //EUTELEOSTEI
          ( 
           // SALMONIFORMES       
           (
            (
             SALMO*,
             (TROUT,ONCORHYNCHUS*)
            ),
            COREGONUS*
           ),
          //PERCOMORPHA
          (
           PARALICHTHYS*,
          //PERCIFORMES
           (
            //PERCOIDEI
            (
             MORONE*,
             SERIOLA*,
             LATES*,
             (GILTHEADSEABREAM,SPARUS*,PAGRUS*)
            ),
            (TILAPIA*,OREOCHROMIS*),           
            (
             CHIONODRACO*,
             (
              NOTOTHENIA_ANGUSTATA,
              NOTOTHENIA_CORIICEPS
             )
            )
           ),
           (
            (FUGU,TAKIFUGU*),
            TETRAODON*          
           ),
           (MEDAKA*,ORYZIAS*)
          )
         )
        ), // END OF BONY FISHES
        //TRETAPODA
        (
         //AMPHIBIANS
         (
          ((FROG,XENOPUS*),SILURANA*, RANA)
         ),
         //AMNIOTA
         (
          DABOIA,       
          // BIRDS
          (
           (SERINUS*,CANARY),
           (
            (TURKEY, MELEAGRIS*),
            (CHICKEN*,GALLUS*)
           ),
           (
            (DUCK,ANAS*,CAIRINA*),
            (GOOSE,ANSER*)
           )
          ),
          //MAMMALS
          (
           //MONOTREMA
           (
            MONOTREMA*
           ),
           //MARSUPIALS
           (
            VOMBATUS*,
            POSUM
           ),
           //EUTHERIA
           (
            //groupIII+groupIV
            (
             //RODENTS+PRIMATES, groupIII 
             (
              //RODENT/RABBIT
              (
               //GLIRES
               (
                (RABBIT,LEPUS*,ORYCTOLAGUS*),
                //RODENTS
                (
                 (
                  (
                   (
                    (
                     COTTONRAT,
                     (RAT,RATTUS*)
                    ),
                    (MOUSE,MUS_MUSCULUS)
                   ),
                   (MESOCRICETUS*,HAMSTER,CRICETULUS*)
                  ),
                  (
                   GLAUCOMYS*,
                   MARMOT
                  )
                 ),
                 //Hystricognathi
                 (
                  (PORCUPINE,HYSTRIX*),
                  (CAVIA*,GUINEAPIG)
                 )                
                ) // END OF RODENTS
               ) // END OF GLIRES
              ), // END OF RODENTS+RABBITS
              //PRIMATES
              (
               //PRIMATES+SHREWS
               (
                //SHREWS
                (
                 TUPAIA*,SHREW
                ),
                //PRIMATES
                (
                 TARSIUS*,
                 //STREPSIRHINI
                 (OTOLEMUR*,PROPITHECUS*),
                 (
                  //PLATYRRHINI
                  (
                   (
                    (
                     (CALLITHRIX*,MARMOSET),
                     (
                      (CEBUS*,CAPUCHIN),
                      (SQUIRRELMONKEY,SAIMIRI*)
                     )
                    ),
                    (
                     CALLICEBUS*,
                     AOTUS*
                    )
                   ),
                   (
                    (
                     ATELES_BELZEBUTH,
                     ATELES_GEOFFROYI
                    ),
                    (
                     CACAJO*,
                     PITHECIA*
                    )
                   ),
                   ALOUATTA*
                  ), // END OF PLATYRRHINI
                  //CATARRHINI 
                  (
                   (HYLOBATES*,GIBBON),
                   (
                    CERCOPITHECUS*,
                    CERCOCEBUS*,
                    (BABOON,PAPIO*),
                    (RHESUS,MACACA*)
                   ),
                   (
                    (PONGO*,ORANGUTAN),
                    (
                     GORILLA*,
                     (
                      (CHIMP,PAN*),
                      (HUMAN,HOMO*)
                     )
                    )
                   )
                  ) // END OF CATARRHINI 
                 )
                ) // END OF PRIMATES
               ) // END OF PRIMATES+SHREWS
              ) // END OF PRIMATES +BATS
             ), // END OF RODENTS+PRIMATES  
             //GroupIV
             (
              //BATS+DERMOPTERA
              (
               //DERMOPTERA
               (
                CYNOCEPHALUS*
               ),
               //BATS
               (
                (
                 CYNOPTERUS*,
                 PTEROPUS*
                ),
                (
                 TAPHOZOUS*,
                 (
                  (
                   MEGADERMA*,
                   HIPPOSIDEROS*
                  ),
                  (
                   TONATIA*,
                   (
                    TADARIDA*,
                    MYOTIS*
                   )
                  )
                 )
                )
               ) // END OF BATS
              ), // END OF BATS+DERMOPTERA
              // DACTYLA+CARNIVORA
              (
               //CARNIVORA
               (
                (SEAL, HALICHOERUS*),
                //FISSIPEDIA
                (
                 MUSTELA*, 
                 (CAT,FELIS*),
                 (CANIS*,DOG)
                )
               ),
               //DACTYLTHINGS
               (
                //PERISSODACTYLA                      
                (
                 (RHINOCEROS,DICEROS*),
                 (
                  (
                   HORSE,
                   EQUUS_ASINUS,
                   EQUUS_CABALLUS
                  )
                 )
                ),
                //ARTIODACTYL+CETACEA
                (
                 CAMELUS*,
                 LAMA*,
                 (
                  (PIG,SUS*),
                  (
                   //RUMINANTIA 
                   (
                    (
                     (
                      (
                       (BOS_TAURUS,BOVIN,COW),
                       BOS_INDICUS
                      ),
                      BOS_GRUNNIENS
                     ),
                     BUBALUS*
                    ),
                    (
                     (
                      (OVIS*,SHEEP),
                      (GOAT,CAPRA*)
                     ),
                     DEER,
                     GAZELLA*
                    )
                   ), // END OF RUMINATIA
                   // HIPPO + CETACEA
                   (
                    HIPPOPOTAMUS*,   
                    //CETACEA
                    (
                     (DOLPHIN, TURSIOPS),
                     (
                      (SPERMWHALE,PHYSETER*),
                      (BLUEWHALE,MEGAPTERA*)
                     )
                    ) // END OF CETACEA
                   ) // END OF HIPPO+CETACEA
                  ) // END OF HIPPO+CETACEA+RUMINANTIA
                 ) // END OF HIPPO+CETACEA+RUMINANTIA+PIG
                ) // END OF CETARTIODACTYLA
               ) // END OF CETARTIODACTYLA+PERISSODACTYLA
              ) // END OF DACTYLA+CARNIVORA
             ) // END OF groupIV
            ) // END OF groupIII_groupIV
           ) // END OF EUTHERIA
          ) // END OF MAMMALS
         ) // END OF AMNIOTA
        ) // END OF TETRAPODA
       ) // END OF GNATHOSTOMA
      ) // END OF VERTEBRATES
      ) // END OF DEUTEROSTOMA
     ) // END OF VERTEBRATES+CELEGANS
    ) // END OF METAZOAN
   ) // END OF FUNGI+ANIMALS
  ) // END OF EUKARYA
 ) // END OF ARCHEA+EUKARYA
) // END OF ALL