"tree of life 1.4" added (for archival purposes)

diff --git a/forester/archive/RIO/tree_of_life_bin_1-4.nhx b/forester/archive/RIO/tree_of_life_bin_1-4.nhx
new file mode 100644 (file)
index 0000000..18ee2ed
--- /dev/null
+++ b/forester/archive/RIO/tree_of_life_bin_1-4.nhx
@@ -0,0 +1,523 @@
+(\r
+(\r
+(\r
+([begin of Eukaryota]\r
+(\r
+(\r
+(\r
+(\r
+(\r
+([begin of eukaryote_crown_group]\r
+(\r
+(\r
+(\r
+([begin of Metazoa]\r
+([begin of Eumetazoa]\r
+([begin of Bilateria]\r
+([begin of Coelomata]\r
+([begin of Deuterostomia]\r
+([begin of Chordata]\r
+(\r
+([begin of Craniata]\r
+([begin of Vertebrata]\r
+([begin of Gnathostomata-jawed_vertebrates]\r
+([begin of Teleostomi]\r
+([begin of Tetrapoda]\r
+([begin of Amniota]\r
+([begin of Mammalia]\r
+([begin of Theria]\r
+([begin of Eutheria]\r
+(\r
+([begin of Primates]\r
+((\r
+([begin of Catarrhini]\r
+(((([&&NHX:S=HUMAN],([&&NHX:S=PANPA],[&&NHX:S=PANTR])),([&&NHX:S=GORBE],[&&NHX:S=GORGO])),[&&NHX:S=PONPY])[&&NHX:S=Hominidae],\r
+((([&&NHX:S=HYLAG],[&&NHX:S=HYLLA]),[&&NHX:S=HYLPI]),[&&NHX:S=HYLSY])[&&NHX:S=Hylobatidae-Gibbons]),\r
+([begin of Cercopithecidae]\r
+(\r
+(\r
+([&&NHX:S=MANSP-Mandrill],\r
+([&&NHX:S=PAPHA-Hamadryas_baboon],[&&NHX:S=PAPAN-Olive_baboon])[&&NHX:S=Papio-Baboons:T=9554]\r
+),\r
+([&&NHX:S=MACMU-Rhesus_macaque],[&&NHX:S=MACFA-Crab_eating_macaque])[&&NHX:S=Macaca:T=9539]\r
+),\r
+[&&NHX:S=CERAE-African-green-monkey:T=9534]\r
+)[&&NHX:S=Cercopithecinae:T=9528],\r
+([&&NHX:S=COLGU-Guereza:T=33548],[&&NHX:S=PYGBI-Black_snub_nosed_monkey:T=61621])[&&NHX:S=Colobinae:T=9569]\r
+)[&&NHX:S=Cercopithecidae-Old_World_monkeys:T=9527]\r
+)[&&NHX:S=Catarrhini:T=9526],\r
+([&&NHX:S=SAISC-Common_squirrel_monkey],[&&NHX:S=BRAAR-Woolly_spider_monkey])[&&NHX:S=Platyrrhini-New_World_Monkeys]),\r
+([&&NHX:S=TARBA],[&&NHX:S=TARSY])[&&NHX:S=Tarsii-Tarsiers]),\r
+(((([&&NHX:S=CHEMA-Lemur],[&&NHX:S=CHEME-Fattailed_dwarf_lemur]),[&&NHX:S=HAPGR-Gray_gentle_lemur]),[&&NHX:S=LEPMU-Weasel_lemur]),([&&NHX:S=GALCR-Thicktailed_galago],[&&NHX:S=PERPO-Potto]))[&&NHX:S=Strepsirhini-lemurs;etc.]\r
+)[&&NHX:S=Primates:T=9443],\r
+(\r
+([begin of Rodentia]\r
+(\r
+([&&NHX:S=MOUSE:T=10090],[&&NHX:S=RAT:T=10116])[&&NHX:S=Murinae-Mice:T=39107],\r
+(\r
+([&&NHX:S=MESAU-Golden_hamster:T=10036],[&&NHX:S=MESBR-Turkish_hamster:T=10037]),\r
+([&&NHX:S=CRIMI-Armenian_hamster:T=10032],[&&NHX:S=CRIGR-Chinese_hamster:T=10029])\r
+)[&&NHX:S=Cricetinae-Hamsters:T=10026]\r
+)[&&NHX:S=Muridae:T=10066],\r
+[&&NHX:S=CAVPO-Guinea_pig:T=10141]\r
+)[&&NHX:S=Rodentia:T=9989],\r
+[&&NHX:S=RABIT:T=9986])),\r
+((([&&NHX:S=CANFA],[&&NHX:S=VULVU-Red_fox]),[&&NHX:S=FELCA-Cat])[&&NHX:S=Carnivora],\r
+([&&NHX:S=HORSE:T=9796],([&&NHX:S=PIG],([&&NHX:S=CEREL-Red_deer:T=9860],([&&NHX:S=BOVIN:T=9913],([&&NHX:S=SHEEP:T=9940],[&&NHX:S=CAPHI-Goat:T=9925])))[&&NHX:S=Ruminantia:T=9845])))\r
+)[&&NHX:S=Eutheria],\r
+(([&&NHX:S=DIDMA-North_American_opossum],[&&NHX:S=MONDO-Shorttailed_grey_opossum]),\r
+[&&NHX:S=SMIMA-Stripefaced_dunnart:T=9302])[&&NHX:S=Metatheria-Marsupials:T=9263 ]\r
+)[&&NHX:S=Theria],\r
+([begin of Prototheria ]\r
+[&&NHX:S=ORNAN-Duckbill_platypus],\r
+([&&NHX:S=ZAGBR-Longbeaked_echidna],[&&NHX:S=TACAC-Australian_echidna])[&&NHX:S=Tachyglossidae]\r
+)[&&NHX:S=Prototheria]\r
+)[&&NHX:S=Mammalia],\r
+\r
+([begin of Sauropsida]\r
+([begin of Testudines]\r
+[&&NHX:S=TRASC-Red-eared_slider_turtle],[&&NHX:S=CHESE-Snapping_turtle]\r
+)[&&NHX:S=Testudines-Turtles],\r
+\r
+([begin of Sauria]\r
+([begin of Archosauria]\r
+([begin of Aves]\r
+[&&NHX:S=CHICK],[&&NHX:S=ANAPL-Domestic_duck]\r
+)[&&NHX:S=Aves],\r
+([begin of Crocodylidae]\r
+[&&NHX:S=ALLMI-American_alligator],[&&NHX:S=CRONI-Nile_crocodile]\r
+)[&&NHX:S=Crocodylidae]\r
+)[&&NHX:S=Archosauria],\r
+\r
+([begin of Lepidosauria]\r
+(\r
+([&&NHX:S=BOACO-Boa_constrictor],[&&NHX:S=TRIAB-Green_pit_viper:T=8765])[&&NHX:S=Serpentes:T=8570],\r
+([&&NHX:S=IGUIG-Common_iguana],[&&NHX:S=ANOCA-Green_anole:T=28377])[&&NHX:S=Iguania:T=8511]\r
+)[&&NHX:S=Squamata:T=8509],\r
+[&&NHX:S=SPHPU-Tuatara]\r
+)[&&NHX:S=Lepidosauria]\r
+)[&&NHX:S=Sauria]\r
+)[&&NHX:S=Sauropsida]\r
+\r
+)[&&NHX:S=Amniota],\r
+\r
+([begin of Amphibia]\r
+([begin of Batrachia]\r
+([&&NHX:S=XENLA],[&&NHX:S=RANCA-Bull_frog])[&&NHX:S=Anura],\r
+([&&NHX:S=CYNPY-Japanese_common_newt],[&&NHX:S=NOTVI-Eastern_newt])[&&NHX:S=Caudata]\r
+)[&&NHX:S=Batrachia],\r
+([&&NHX:S=DERME],[&&NHX:S=GRAAL])[&&NHX:S=Gymnophiona]\r
+)[&&NHX:S=Amphibia]\r
+\r
+)[&&NHX:S=Tetrapoda],\r
+\r
+(\r
+([&&NHX:S=ONCMY-Rainbow_trout:T=8022],[&&NHX:S=FUGRU:T=31033]),\r
+(\r
+[&&NHX:S=BRARE-Zebrafish:T=7955],([&&NHX:S=CYPCA-Common_carp:T=7962],[&&NHX:S=CARAU-Goldfish:T=7957])[&&NHX:S=Cyprininae:T=39560]\r
+)[&&NHX:S=Ostariophysi:T=32519]\r
+)[&&NHX:S=Euteleostei:T=32447]\r
+)[&&NHX:S=Teleostomi:T=117570],\r
+\r
+([&&NHX:S=ALOVU-Thresher_shark],[&&NHX:S=DASSA-Atlantic_stingray])[&&NHX:S=Chondrichthyes:T=7777]\r
+\r
+)[&&NHX:S=Gnathostomata-jawed_vertebrates],\r
+\r
+([&&NHX:S=LAMFL-River_lamprey],[&&NHX:S=LAMJA-Japanese_lamprey])[&&NHX:S=Hyperoartia-lampreys ]\r
+\r
+)[&&NHX:S=Vertebrata],\r
+([&&NHX:S=EPTBU-Inshore hagfish:T=7764],[&&NHX:S=EPTST-Pacific_hagfish:T=7765])[&&NHX:S=Hyperotreti]\r
+)[&&NHX:S=Craniata],\r
+([&&NHX:S=BRAFL-Florida_lancelet:T=7739],[&&NHX:S=BRALA-Amphioxus:T=7740])[&&NHX:S=Cephalochordata]\r
+),\r
+([&&NHX:S=CIOIN:T=7719],[&&NHX:S=CIOSA:T=51511])[&&NHX:S=Urochordata-Tunicates:T=7712]\r
+)[&&NHX:S=Chordata],\r
+([begin of Echinodermata]\r
+([&&NHX:S=STRPU-Purple_sea_urchin:T=7668],[&&NHX:S=ANTCR:T=7629])[&&NHX:S=Echinoidea-Sea_urchins:T=7625],\r
+[&&NHX:S=ASTPE-Starfish:T=7594]\r
+)[&&NHX:S=Echinodermata:T=7586]\r
+)[&&NHX:S=Deuterostomia:T=33511],\r
+([begin of Protostomia]\r
+(\r
+[&&NHX:S=APLCA-California_sea_hare:T=6500],[&&NHX:S=LYMST-Great_pond_snail:T=6523]\r
+)[&&NHX:S=Mollusca:T=6447],\r
+[&&NHX:S=HIRME-Medicinal_leech:T=6421]\r
+)[&&NHX:S=Protostomia:T=33317]\r
+)[&&NHX:S=Coelomata:T=33316],\r
+\r
+([begin of arthropod/nematode group]\r
+\r
+([begin of Arthropoda]\r
+(\r
+(\r
+([&&NHX:S=DROME:T=7227],[&&NHX:S=DROVI-Drosophila_virilis:T=7244]),\r
+[&&NHX:S=MUSDO-House_fly:T=7370]\r
+)\r
+,[&&NHX:S=BLAGE-German_cockroach:T=6973]\r
+)[&&NHX:S=Insecta:T=50557],\r
+(\r
+([&&NHX:S=HOMAM-American_lobster:T=6706],[&&NHX:S=CARMA-Green_crab:T=6759])[&&NHX:S=Crustacea:T=6657]\r
+,[&&NHX:S=LIMPO-Atlantic_horseshoe_crab:T=6850]\r
+)\r
+)[&&NHX:S=Arthropoda:T=6656],\r
+\r
+([begin of Nematoda]\r
+(\r
+([&&NHX:S=CAEEL:T=6239],[&&NHX:S=CAEBR:T=6238])[&&NHX:S=Rhabditidae:T=6243],\r
+[&&NHX:S=HAECO-Haemonchus_contortus:T=6289]\r
+)[&&NHX:S=Rhabditida:T=6236],\r
+[&&NHX:S=ASCSU-Pig_roundworm:T=6253]\r
+)[&&NHX:S=Nematoda:T=6231]\r
+\r
+)[arthropod/nematode group]\r
+\r
+)[&&NHX:S=Bilateria:T=33213],\r
+\r
+(\r
+([&&NHX:S=ACTEQ-European_sea_anemone:T=6106],[&&NHX:S=ANTEL-Sea_anemone:T=6110])[&&NHX:S=Actiniaria-Sea_anemones:T=6103],\r
+[&&NHX:S=TRICY-Jellyfish:T=6141] \r
+)[&&NHX:S=Cnidaria:T=6073]\r
+\r
+\r
+)[&&NHX:S=Eumetazoa:T=6072],\r
+\r
+(\r
+[&&NHX:S=EPHMU-Muellers_freshwater_sponge:T=6052],[&&NHX:S=GEOCY-Geodia_cydonium:T=6047]\r
+)[&&NHX:S=Porifera-Sponges:T=6040]\r
+\r
+)[&&NHX:S=Metazoa:T=33208],\r
+\r
+\r
+\r
+([begin of Fungi]\r
+\r
+(\r
+([begin of Basidiomycota]\r
+(\r
+([&&NHX:S=LENED-Shiitake_mushroom:T=5353],[&&NHX:S=AGABI-Common_mushroom:T=5341])[&&NHX:S=Agaricales:T=5338],\r
+[&&NHX:S=PHACH-Phanerochaete_chrysosporium:T=5306]\r
+)[&&NHX:S=Hymenomycetes:T=5302],\r
+([&&NHX:S=USTMA-Smut_fungus:T=5270],[&&NHX:S=USTSP-Smut_fungus:T=5271])[&&NHX:S=Ustilago:T=5269]\r
+)[&&NHX:S=Basidiomycota],\r
+([begin of Ascomycota]\r
+(\r
+(\r
+(\r
+([&&NHX:S=YEAST:T=4932],[&&NHX:S=SACKL:T=4934])[&&NHX:S=Saccharomyces:T=4930],\r
+([&&NHX:S=KLULA:T=28985],[&&NHX:S=KLUMA:T=4911])[&&NHX:S=Kluyveromyces:T=4910][,\r
+([&&NHX:S=PICPA-Pichia_pastoris:T=4922],[&&NHX:S=PICJA-Pichia_jadinii:T=4903],[&&NHX:S=PICAN-Pichia_angusta:T=4905])[&&NHX:S=Pichia:T=4919]\r
+,[&&NHX:S=YAMOH-Yamadazyma_ohmeri:T=34356]]\r
+)[&&NHX:S=Saccharomycetaceae:T=4893],\r
+(\r
+[&&NHX:S=CANAL:T=5476],[&&NHX:S=CANTR:T=5482][,[&&NHX:S=CANGA-Candida_glabrata:T=5478],[&&NHX:S=CANMA-Candida_maltosa:T=5479],\r
+[&&NHX:S=CANBO-Candida boidinii:T=5477]]\r
+)[&&NHX:S=anamorphic_Saccharomycetales:T=118267]\r
+)[&&NHX:S=Saccharomycetes:T=4891],\r
+(\r
+([&&NHX:S=NEUCR:T=5141],[&&NHX:S=NEUIN:T=5142])[&&NHX:S=Sordariales:T=5139],\r
+([&&NHX:S=ASPNG:T=5061],[&&NHX:S=EMENI:T=5072])[&&NHX:S=Eurotiales:T=5042])\r
+),\r
+([&&NHX:S=SCHPO:T=4896],[&&NHX:S=PNECA-Pneumocystis_carinii:T=4754])\r
+)[&&NHX:S=Ascomycota]\r
+),\r
+(\r
+[&&NHX:S=MORPI-Mortierella_alpina:T=64518],[&&NHX:S=MUCRO-Mucor_rouxii:T=29923]\r
+)[&&NHX:S=Zygomycota:T=4825]\r
+)[&&NHX:S=Fungi]\r
+),\r
+\r
+([begin of Viridiplantae]\r
+([begin of Streptophyta]\r
+([begin of Charophyta/Embryophyta group]\r
+([begin of Embryophyta]\r
+([begin of Tracheophyta]\r
+([begin of Spermatophyta]\r
+(\r
+([begin of Magnoliophyta]\r
+([begin of Liliopsida]\r
+\r
+(\r
+([&&NHX:S=MAIZE:T=4577],[&&NHX:S=SORBI-Sorghum_bicolor:T=4558])[&&NHX:S=Panicoideae:T=147369],\r
+(\r
+(\r
+([&&NHX:S=HORVU-Barley:T=4513],[&&NHX:S=WHEAT-Triticum_aestivum:T=4565])[&&NHX:S=Triticeae:T=147389],\r
+[&&NHX:S=AVESA-Oat:T=4498]\r
+)[&&NHX:S=Pooideae:T=147368],\r
+[&&NHX:S=ORYSA-Rice:T=4530]\r
+)\r
+)[&&NHX:S=Poaceae-Grasses:T=4479],\r
+\r
+(\r
+[&&NHX:S=ALLCE-Onion:T=4679],[&&NHX:S=ASPOF-Garden_asparagus:T=4686]\r
+)[&&NHX:S=Asparagales:T=73496]\r
+\r
+)[&&NHX:S=Liliopsida-Monocotyledons:T=4447],\r
+\r
+([begin of eudicotyledons]\r
+(([&&NHX:S=TOBAC-Common_tobacco:T=4097],[&&NHX:S=NICPL-Curled_leaved_tobacco:T=4092])[&&NHX:S=Nicotiana:T=4085],\r
+([&&NHX:S=LYCES-Tomato:T=4081],[&&NHX:S=SOLTU-Potato:T=4113])[&&NHX:S=Solanum:T=4107])[&&NHX:S=Asteridae:T=71274],\r
+(\r
+\r
+([begin of Rosidae]\r
+\r
+(\r
+([&&NHX:S=SOYBN:T=3847],[&&NHX:S=PEA:T=3888][,[&&NHX:S=MEDSA-Alfalfa:T=3879]])[&&NHX:S=Fabales:T=72025],\r
+([&&NHX:S=CUCSA-Cucumber:T=3659],[&&NHX:S=CUCMA-Winter_squash:T=3661])[&&NHX:S=Cucurbitales:T=71239]\r
+)[&&NHX:S=eurosids I:T=91835],\r
+\r
+(\r
+(\r
+([&&NHX:S=BRANA-Rape:T=3708],[&&NHX:S=BRACM-Field_mustard:T=3711])[&&NHX:S=Brassica:T=3705]\r
+,[&&NHX:S=ARATH:T=3702]\r
+)[&&NHX:S=Brassicaceae-Mustard_family:T=3700],\r
+(\r
+([&&NHX:S=CITSI-Citrus_sinensis:T=2711],[&&NHX:S=CITUN-Citrus_unshiu:T=55188])[&&NHX:S=Sapindales:T=41937],\r
+([&&NHX:S=GOSHI-Upland_cotton:T=3635],[&&NHX:S=THECC-Cacao:T=3641])[&&NHX:S=Malvales:T=41938]\r
+)\r
+)[&&NHX:S=eurosids II:T=91836]\r
+\r
+)[&&NHX:S=Rosidae:T=71275],\r
+\r
+(\r
+[&&NHX:S=BETVU-Beet:T=3555],[&&NHX:S=SPIOL-Spinach:T=3562]\r
+)[&&NHX:S=Caryophyllidae:T=71273]\r
+\r
+)\r
+)[&&NHX:S=eudicotyledons:T=71240]\r
+)[&&NHX:S=Magnoliophyta-Flowering_plants:T=3398],\r
+\r
+(\r
+[&&NHX:S=EPHTW-Ephedra_tweediana:T=3390],[&&NHX:S=WELMI-Welwitschia_mirabilis:T=3377]\r
+)[&&NHX:S=Gnetophyta:T=58022]\r
+\r
+)[a suspicious grouping], \r
+\r
+(\r
+\r
+(\r
+(\r
+(\r
+[&&NHX:S=PSEMZ-Douglas_fir:T=3357],[&&NHX:S=PINTH-Japanese_black_pine:T=3350]\r
+)[&&NHX:S=Pinaceae:T=3318],\r
+[&&NHX:S=JUNVI-Red_cedar:T=39584]\r
+)[&&NHX:S=Coniferales:T=3313],\r
+[&&NHX:S=GINBI-Ginkgo_biloba:T=3311]\r
+)[a suspicious grouping],\r
+\r
+([&&NHX:S=ZAMFU-Zamia_furfuracea:T=42329],[&&NHX:S=ZAMFI-Zamia_fischeri:T=34342])[&&NHX:S=Cycadales:T=3297]\r
+)[a suspicious grouping]\r
+\r
+)[&&NHX:S=Spermatophyta-Seed_plants:T=58024],\r
+\r
+[&&NHX:S=EQUAR-Field_horsetail:T=3258]\r
+\r
+)[&&NHX:S=Tracheophyta-Vascular_plants:T=58023],\r
+\r
+([begin of Bryophyta]\r
+[&&NHX:S=CERPU-Ceratodon_purpureus:T=3225],[&&NHX:S=PHYPA-Physcomitrella_patens:T=3218]\r
+)[&&NHX:S=Bryophyta-Mosses:T=3208]\r
+\r
+)[&&NHX:S=Embryophyta-Land_plants:T=3193],\r
+\r
+[&&NHX:S=COLOB-Coleochaete_orbicularis:T=3124]\r
+\r
+)[&&NHX:S=Charophyta_Embryophyta_group:T=131221],\r
+\r
+[&&NHX:S=MESVI-Mesostigma_viride:T=41882]\r
+\r
+)[&&NHX:S=Streptophyta:T=35493],\r
+\r
+([begin of Chlorophyta]\r
+(\r
+[&&NHX:S=VOLCA-Volvox_carteri:T=3067],\r
+([&&NHX:S=CHLEU-Chlamydomonas_eugametos:T=3053],[&&NHX:S=CHLRE-Chlamydomonas_reinhardtii:T=3055])[&&NHX:S=Chlamydomonas:T=3052]\r
+)[&&NHX:S=Chlorophyceae:T=3166],\r
+[&&NHX:S=CHLVU-Chlorella_vulgaris:T=3077]\r
+)[&&NHX:S=Chlorophyta-Green_algae:T=3041]\r
+\r
+)[&&NHX:S=Viridiplantae:T=33090]\r
+),\r
+([&&NHX:S=ACHAM-Achlya_ambisexualis:T=4768],[&&NHX:S=COSCS-Costaria_costata:T=2872])[&&NHX:S=Stramenopiles:T=33634]\r
+),\r
+(\r
+([&&NHX:S=BABBO-Babesia_bovis:T=5865],[&&NHX:S=PLAFA-Plasmodium_falciparum:T=5833])\r
+,[&&NHX:S=PARTE-Paramecium_tetraurelia:T=5888]\r
+)[&&NHX:S=Alveolata:T=33630]\r
+),\r
+([&&NHX:S=PORPU-Porphyra_purpurea:T=2787],[&&NHX:S=CYACA-Cyanidium_caldarium:T=2771])[&&NHX:S=Rhodophyta-Red_algae:T=2763]\r
+)[&&NHX:S=eukaryote_crown_group:T=33089],\r
+[&&NHX:S=DICDI-Dictyostelium_discoideum:T=44689]\r
+),\r
+[&&NHX:S=ENTHI-Entamoeba_histolytica:T=5759]),\r
+(\r
+([&&NHX:S=TRYBB-Trypanosoma_brucei_brucei:T=5702],[&&NHX:S=LEIMA-Leishmania_major:T=5664])\r
+,[&&NHX:S=EUGGR-Euglena_gracilis:T=3039])[&&NHX:S=Euglenozoa:T=33682]\r
+),\r
+[&&NHX:S=PHYPO-Physarum_polycephalum:T=5791]\r
+),\r
+([&&NHX:S=GIALA-Giardia_intestinalis:T=5741],[&&NHX:S=SPIVO-Spironucleus_vortens:T=58336])[&&NHX:S=Diplomonadida:T=5738]\r
+\r
+)[&&NHX:S=Eukaryota:T=2759],\r
+\r
+([begin of Archaea]\r
+\r
+([begin of Crenarchaeota]\r
+([&&NHX:S=SULAC-Sulfolobus_acidocaldarius:T=2285],[&&NHX:S=SULSO-Sulfolobus_solfataricus:T=2287])[&&NHX:S=Sulfolobus:T=2284],\r
+[&&NHX:S=AERPE-Aeropyrum_pernix:T=56636]\r
+)[&&NHX:S=Crenarchaeota:T=28889],\r
+\r
+([begin of Euryarchaeota]\r
+(\r
+(\r
+([&&NHX:S=METJA-Methanococcus_jannaschii:T=2190],[&&NHX:S=METVA-Methanococcus_vannielii:T=2187])[&&NHX:S=Methanococcales:T=2182],\r
+(\r
+[&&NHX:S=ARCFU-Archaeoglobus_fulgidus:T=2234],\r
+[&&NHX:S=THEAC-Thermoplasma_acidophilum:T=2303]\r
+)\r
+),\r
+([&&NHX:S=PYRFU-Pyrococcus_furiosus:T=2261],[&&NHX:S=PYRHO-Pyrococcus_horikoshii:T=53953])[&&NHX:S=Thermococcales:T=2258]\r
+),\r
+([&&NHX:S=METTH-Methanobacterium_thermoautotrophicum:T=2166],[&&NHX:S=METFE-Methanothermus_fervidus:T=2180])[&&NHX:S=Methanobacteriales:T=2158]\r
+)[&&NHX:S=Euryarchaeota:T=28890]\r
+\r
+)[&&NHX:S=Archaea:T=2157]\r
+\r
+),\r
+\r
+\r
+([begin of Bacteria]\r
+\r
+([&&NHX:S=AQUAE-Aquifex_aeolicus:T=63363],[&&NHX:S=AQUPY-Aquifex_pyrophilus:T=2714])[&&NHX:S=Aquificales:T=32069],\r
+(\r
+([&&NHX:S=THEMA-Thermotoga_maritima:T=2336],[&&NHX:S=THENE-Thermotoga_neapolitana:T=2337])[&&NHX:S=Thermotogales:T=2419],\r
+(\r
+(([&&NHX:S=THEAQ-Thermus_aquaticus:T=271],[&&NHX:S=THETH-Thermus_thermophilus:T=274])[&&NHX:S=Thermus_group:T=68933],\r
+[&&NHX:S=DEIRA-Deinococcus_radiodurans:T=1299])[&&NHX:S=Thermus/Deinococcus_group:T=1297],\r
+\r
+(\r
+\r
+([begin of Firmicutes-grampositive_bacteria]\r
+([begin of Bacillus/Clostridium_group]\r
+(\r
+(\r
+(\r
+(\r
+[&&NHX:S=BACSU-Bacillus_subtilis:T=1423],[&&NHX:S=BACST-Bacillus_stearothermophilus:T=1422][,[&&NHX:S=BACCO-Bacillus_coagulans:T=1398]\r
+,[&&NHX:S=BACCA-Bacillus_caldotenax:T=1395],[&&NHX:S=BACME-Bacillus megaterium:T=1404]]\r
+)[&&NHX:S=Bacillus:T=1386],\r
+[&&NHX:S=STAAU-Staphylococcus_aureus:T=1280]\r
+)[&&NHX:S=Bacillus/Staphylococcus_group:T=1385],\r
+(\r
+([&&NHX:S=STRMU-Streptococcus_mutans:T=1309],[&&NHX:S=STRPN-Streptococcus_pneumoniae:T=1313])[&&NHX:S=Streptococcus:T=1301],\r
+[&&NHX:S=LACLA-Lactococcus_lactis_lactis:T=1360]\r
+)[&&NHX:S=Streptococcaceae:T=1300]\r
+)[&&NHX:S=Bacillus/Lactobacillus/Streptococcus_group:T=91061],\r
+[&&NHX:S=CLOPA-Clostridium_pasteurianum:T=1501]\r
+),[these paranthesis are -- even more -- questionable]\r
+(\r
+([&&NHX:S=MYCGE-Mycoplasma_genitalium:T=2097],[&&NHX:S=MYCPN-Mycoplasma_pneumoniae:T=2104])[&&NHX:S=Mycoplasmatales:T=2085],\r
+[&&NHX:S=ACHLA-Acholeplasma_laidlawii:T=2148]\r
+)[&&NHX:S=Mollicutes:T=31969]\r
+)[&&NHX:S=Bacillus/Clostridium_group:T=31968],\r
+([begin of Actinobacteria]\r
+(\r
+(\r
+([&&NHX:S=MYCTU-Mycobacterium_tuberculosis:T=1773],[&&NHX:S=MYCBO-Mycobacterium_bovis:T=1765])[&&NHX:S=Mycobacterium_tuberculosis_complex:T=77643],\r
+[&&NHX:S=MYCLE-Mycobacterium_leprae:T=1769]\r
+[,[&&NHX:S=MYCSM-Mycobacterium_smegmatis:T=1772]]\r
+)[&&NHX:S=Mycobacterium:T=1763],\r
+[&&NHX:S=CORGL-Corynebacterium_glutamicum:T=1718]\r
+)[&&NHX:S=Corynebacterineae:T=85007],\r
+[&&NHX:S=PROFR-Propionibacterium_freudenreichii_shermanii:T=1752]\r
+)[&&NHX:S=Actinobacteria:T=1760]\r
+)[&&NHX:S=Firmicutes-grampositive_bacteria:T=1239],\r
+\r
+([begin of group of Cyanobacteria, Proteobacteria, Chlamydiales, Green_sulfur, Spirochaetales ?]\r
+(\r
+(\r
+([&&NHX:S=CHLPN-Chlamydophila_pneumoniae:T=83558],[&&NHX:S=CHLTR-Chlamydia_trachomatis:T=813])[&&NHX:S=Chlamydiales/Verrucomicrobia_group:T=51290],\r
+([&&NHX:S=CHLLI-Chlorobium_limicola:T=1092],[&&NHX:S=CHLVI-Chlorobium_vibrioforme:T=1098])[&&NHX:S=Green_sulfur_bacteria:T=1090]\r
+),\r
+([&&NHX:S=LEPIN-Leptospira_interrogans:T=173],[&&NHX:S=BORBU-Borrelia_burgdorferi:T=139])[&&NHX:S=Spirochaetales:T=136]\r
+),\r
+\r
+([begin of group of Cyanobacteria and Proteobacteria ?]\r
+\r
+([begin of Cyanobacteria]\r
+(\r
+([&&NHX:S=SYNP2-PCC_7002:T=32049],[&&NHX:S=SYNP6-PCC_6301:T=1139][,[&&NHX:S=SYNEL:T=32046],[&&NHX:S=SYNLI:T=33070]])[&&NHX:S=Synechococcus:T=1129],\r
+([&&NHX:S=SYNY1-PCC_6701:T=1144],[&&NHX:S=SYNY3-PCC_6803:T=1148][,[&&NHX:S=SYNY4-PCC_6714:T=1147],[&&NHX:S=SYNY8-PCC_6308:T=113355]])[&&NHX:S=Synechocystis:T=1142]\r
+)[&&NHX:S=Chroococcales:T=1118],\r
+[&&NHX:S=ANASP-Anabaena_PCC_7120:T=1174]\r
+[,[&&NHX:S=SPIPL-Spirulina_platensis:T=1156]]\r
+)[&&NHX:S=Cyanobacteria:T=1117],\r
+\r
+([begin of Proteobacteria]\r
+\r
+(\r
+(\r
+\r
+([begin of gamma_subdivision]\r
+(\r
+(\r
+(\r
+[&&NHX:S=SALTY-Salmonella_typhimurium:T=602],[&&NHX:S=ECOLI-Escherichia_coli:T=562][,[&&NHX:S=KLEPN-Klebsiella_pneumoniae:T=573]]\r
+)[&&NHX:S=Enterobacteriaceae:T=91347],\r
+[&&NHX:S=BUCAP-Buchnera_aphidicola:T=98794]\r
+)[&&NHX:S=Enterobacteriaceae_and_related_endosymbionts:T=91347],\r
+[&&NHX:S=HAEIN-Haemophilus_influenzae:T=727]\r
+[,[&&NHX:S=AZOVI-Azotobacter_vinelandii:T=354]\r
+,([&&NHX:S=COXBU-Coxiella_burnetii:T=777],[&&NHX:S=LEGPN-Legionella_pneumophila:T=446])[&&NHX:S=Legionellaceae_group:T=118969]]\r
+),[these paranthesis are -- even more -- questionable]\r
+(\r
+[&&NHX:S=PSEPU-Pseudomonas_putida:T=303],[&&NHX:S=PSEAE-Pseudomonas_aeruginosa:T=287]\r
+)[&&NHX:S=Pseudomonas_group:T=72274]\r
+)[&&NHX:S=gamma_subdivision:T=1236],\r
+\r
+([begin of beta_subdivision]\r
+[&&NHX:S=ALCEU-Alcaligenes_eutrophus:T=510],\r
+([&&NHX:S=NEIME-Neisseria_meningitidis:T=487],[&&NHX:S=NEILA-Neisseria_lactamica:T=486])\r
+)[&&NHX:S=beta_subdivision:T=28216]\r
+\r
+),\r
+\r
+([begin of alpha_subdivision]\r
+([?]\r
+(\r
+([&&NHX:S=RHOCA-Rhodobacter_capsulatus:T=1061],[&&NHX:S=RHOSH-Rhodobacter_sphaeroides:T=1063])[&&NHX:S=Rhodobacter:T=1060],\r
+[&&NHX:S=PARDE-Paracoccus_denitrificans:T=266]\r
+)[&&NHX:S=Rhodobacter_group:T=31989],\r
+\r
+(\r
+(\r
+([&&NHX:S=RHILE-Rhizobium_leguminosarum:T=384],[&&NHX:S=RHITR-Rhizobium_tropici:T=398])[&&NHX:S=Rhizobium:T=379],\r
+[&&NHX:S=AGRTU-Agrobacterium_tumefaciens:T=362]\r
+)[&&NHX:S=Rhizobiaceae:T=82115],\r
+(\r
+[&&NHX:S=BARBA-Bartonella_bacilliformis:T=774],[&&NHX:S=BARQU-Bartonella_quintana:T=803]\r
+)[&&NHX:S=Bartonellaceae:T=772]\r
+)[&&NHX:S=Rhizobiaceae_group:T=356]\r
+),\r
+(\r
+([&&NHX:S=RICPR-Rickettsia_prowazekii:T=782],[&&NHX:S=RICTY-Rickettsia_typhi:T=785])[&&NHX:S=typhus_group:T=114292],\r
+[&&NHX:S=RICRI-Rickettsia_rickettsii:T=783]\r
+)[&&NHX:S=Rickettsiales:T=766]\r
+)[&&NHX:S=alpha_subdivision:T=28211]\r
+),\r
+\r
+([begin of delta/epsilon_subdivisions]\r
+([&&NHX:S=MYXXA-Myxococcus_xanthus:T=34],[&&NHX:S=DESDE-Desulfovibrio_desulfuricans:T=876])[&&NHX:S=delta_subdivision:T=28221],\r
+([&&NHX:S=CAMCO-Campylobacter_coli:T=195],[&&NHX:S=HELPY-Helicobacter_pylori:T=210])[&&NHX:S=epsilon_subdivision:T=29547]\r
+)[&&NHX:S=delta/epsilon_subdivisions:T=68525]\r
+\r
+)[&&NHX:S=Proteobacteria:T=1224]\r
+\r
+)[group of Cyanobacteria and Proteobacteria ?]\r
+\r
+)[group of Cyanobacteria, Proteobacteria, Chlamydiales, Green_sulfur, Spirochaetales ?]\r
+\r
+)\r
+)\r
+)\r
+)[&&NHX:S=Bacteria:T=2]);\r
+\r