From b2c02301e8a65eb1d87341cc6078bbd965d7d785 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 24 Feb 2011 21:10:42 +0000 Subject: [PATCH] "tree of life 1.4" added (for archival purposes) --- forester/archive/RIO/tree_of_life_bin_1-4.nhx | 523 +++++++++++++++++++++++++ 1 file changed, 523 insertions(+) create mode 100644 forester/archive/RIO/tree_of_life_bin_1-4.nhx 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 index 0000000..18ee2ed --- /dev/null +++ b/forester/archive/RIO/tree_of_life_bin_1-4.nhx @@ -0,0 +1,523 @@ +( +( +( +([begin of Eukaryota] +( +( +( +( +( +([begin of eukaryote_crown_group] +( +( +( +([begin of Metazoa] +([begin of Eumetazoa] +([begin of Bilateria] +([begin of Coelomata] +([begin of Deuterostomia] +([begin of Chordata] +( +([begin of Craniata] +([begin of Vertebrata] +([begin of Gnathostomata-jawed_vertebrates] +([begin of Teleostomi] +([begin of Tetrapoda] +([begin of Amniota] +([begin of Mammalia] +([begin of Theria] +([begin of Eutheria] +( +([begin of Primates] +(( +([begin of Catarrhini] +(((([&&NHX:S=HUMAN],([&&NHX:S=PANPA],[&&NHX:S=PANTR])),([&&NHX:S=GORBE],[&&NHX:S=GORGO])),[&&NHX:S=PONPY])[&&NHX:S=Hominidae], +((([&&NHX:S=HYLAG],[&&NHX:S=HYLLA]),[&&NHX:S=HYLPI]),[&&NHX:S=HYLSY])[&&NHX:S=Hylobatidae-Gibbons]), +([begin of Cercopithecidae] +( +( +([&&NHX:S=MANSP-Mandrill], +([&&NHX:S=PAPHA-Hamadryas_baboon],[&&NHX:S=PAPAN-Olive_baboon])[&&NHX:S=Papio-Baboons:T=9554] +), +([&&NHX:S=MACMU-Rhesus_macaque],[&&NHX:S=MACFA-Crab_eating_macaque])[&&NHX:S=Macaca:T=9539] +), +[&&NHX:S=CERAE-African-green-monkey:T=9534] +)[&&NHX:S=Cercopithecinae:T=9528], +([&&NHX:S=COLGU-Guereza:T=33548],[&&NHX:S=PYGBI-Black_snub_nosed_monkey:T=61621])[&&NHX:S=Colobinae:T=9569] +)[&&NHX:S=Cercopithecidae-Old_World_monkeys:T=9527] +)[&&NHX:S=Catarrhini:T=9526], +([&&NHX:S=SAISC-Common_squirrel_monkey],[&&NHX:S=BRAAR-Woolly_spider_monkey])[&&NHX:S=Platyrrhini-New_World_Monkeys]), +([&&NHX:S=TARBA],[&&NHX:S=TARSY])[&&NHX:S=Tarsii-Tarsiers]), +(((([&&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.] +)[&&NHX:S=Primates:T=9443], +( +([begin of Rodentia] +( +([&&NHX:S=MOUSE:T=10090],[&&NHX:S=RAT:T=10116])[&&NHX:S=Murinae-Mice:T=39107], +( +([&&NHX:S=MESAU-Golden_hamster:T=10036],[&&NHX:S=MESBR-Turkish_hamster:T=10037]), +([&&NHX:S=CRIMI-Armenian_hamster:T=10032],[&&NHX:S=CRIGR-Chinese_hamster:T=10029]) +)[&&NHX:S=Cricetinae-Hamsters:T=10026] +)[&&NHX:S=Muridae:T=10066], +[&&NHX:S=CAVPO-Guinea_pig:T=10141] +)[&&NHX:S=Rodentia:T=9989], +[&&NHX:S=RABIT:T=9986])), +((([&&NHX:S=CANFA],[&&NHX:S=VULVU-Red_fox]),[&&NHX:S=FELCA-Cat])[&&NHX:S=Carnivora], +([&&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]))) +)[&&NHX:S=Eutheria], +(([&&NHX:S=DIDMA-North_American_opossum],[&&NHX:S=MONDO-Shorttailed_grey_opossum]), +[&&NHX:S=SMIMA-Stripefaced_dunnart:T=9302])[&&NHX:S=Metatheria-Marsupials:T=9263 ] +)[&&NHX:S=Theria], +([begin of Prototheria ] +[&&NHX:S=ORNAN-Duckbill_platypus], +([&&NHX:S=ZAGBR-Longbeaked_echidna],[&&NHX:S=TACAC-Australian_echidna])[&&NHX:S=Tachyglossidae] +)[&&NHX:S=Prototheria] +)[&&NHX:S=Mammalia], + +([begin of Sauropsida] +([begin of Testudines] +[&&NHX:S=TRASC-Red-eared_slider_turtle],[&&NHX:S=CHESE-Snapping_turtle] +)[&&NHX:S=Testudines-Turtles], + +([begin of Sauria] +([begin of Archosauria] +([begin of Aves] +[&&NHX:S=CHICK],[&&NHX:S=ANAPL-Domestic_duck] +)[&&NHX:S=Aves], +([begin of Crocodylidae] +[&&NHX:S=ALLMI-American_alligator],[&&NHX:S=CRONI-Nile_crocodile] +)[&&NHX:S=Crocodylidae] +)[&&NHX:S=Archosauria], + +([begin of Lepidosauria] +( +([&&NHX:S=BOACO-Boa_constrictor],[&&NHX:S=TRIAB-Green_pit_viper:T=8765])[&&NHX:S=Serpentes:T=8570], +([&&NHX:S=IGUIG-Common_iguana],[&&NHX:S=ANOCA-Green_anole:T=28377])[&&NHX:S=Iguania:T=8511] +)[&&NHX:S=Squamata:T=8509], +[&&NHX:S=SPHPU-Tuatara] +)[&&NHX:S=Lepidosauria] +)[&&NHX:S=Sauria] +)[&&NHX:S=Sauropsida] + +)[&&NHX:S=Amniota], + +([begin of Amphibia] +([begin of Batrachia] +([&&NHX:S=XENLA],[&&NHX:S=RANCA-Bull_frog])[&&NHX:S=Anura], +([&&NHX:S=CYNPY-Japanese_common_newt],[&&NHX:S=NOTVI-Eastern_newt])[&&NHX:S=Caudata] +)[&&NHX:S=Batrachia], +([&&NHX:S=DERME],[&&NHX:S=GRAAL])[&&NHX:S=Gymnophiona] +)[&&NHX:S=Amphibia] + +)[&&NHX:S=Tetrapoda], + +( +([&&NHX:S=ONCMY-Rainbow_trout:T=8022],[&&NHX:S=FUGRU:T=31033]), +( +[&&NHX:S=BRARE-Zebrafish:T=7955],([&&NHX:S=CYPCA-Common_carp:T=7962],[&&NHX:S=CARAU-Goldfish:T=7957])[&&NHX:S=Cyprininae:T=39560] +)[&&NHX:S=Ostariophysi:T=32519] +)[&&NHX:S=Euteleostei:T=32447] +)[&&NHX:S=Teleostomi:T=117570], + +([&&NHX:S=ALOVU-Thresher_shark],[&&NHX:S=DASSA-Atlantic_stingray])[&&NHX:S=Chondrichthyes:T=7777] + +)[&&NHX:S=Gnathostomata-jawed_vertebrates], + +([&&NHX:S=LAMFL-River_lamprey],[&&NHX:S=LAMJA-Japanese_lamprey])[&&NHX:S=Hyperoartia-lampreys ] + +)[&&NHX:S=Vertebrata], +([&&NHX:S=EPTBU-Inshore hagfish:T=7764],[&&NHX:S=EPTST-Pacific_hagfish:T=7765])[&&NHX:S=Hyperotreti] +)[&&NHX:S=Craniata], +([&&NHX:S=BRAFL-Florida_lancelet:T=7739],[&&NHX:S=BRALA-Amphioxus:T=7740])[&&NHX:S=Cephalochordata] +), +([&&NHX:S=CIOIN:T=7719],[&&NHX:S=CIOSA:T=51511])[&&NHX:S=Urochordata-Tunicates:T=7712] +)[&&NHX:S=Chordata], +([begin of Echinodermata] +([&&NHX:S=STRPU-Purple_sea_urchin:T=7668],[&&NHX:S=ANTCR:T=7629])[&&NHX:S=Echinoidea-Sea_urchins:T=7625], +[&&NHX:S=ASTPE-Starfish:T=7594] +)[&&NHX:S=Echinodermata:T=7586] +)[&&NHX:S=Deuterostomia:T=33511], +([begin of Protostomia] +( +[&&NHX:S=APLCA-California_sea_hare:T=6500],[&&NHX:S=LYMST-Great_pond_snail:T=6523] +)[&&NHX:S=Mollusca:T=6447], +[&&NHX:S=HIRME-Medicinal_leech:T=6421] +)[&&NHX:S=Protostomia:T=33317] +)[&&NHX:S=Coelomata:T=33316], + +([begin of arthropod/nematode group] + +([begin of Arthropoda] +( +( +([&&NHX:S=DROME:T=7227],[&&NHX:S=DROVI-Drosophila_virilis:T=7244]), +[&&NHX:S=MUSDO-House_fly:T=7370] +) +,[&&NHX:S=BLAGE-German_cockroach:T=6973] +)[&&NHX:S=Insecta:T=50557], +( +([&&NHX:S=HOMAM-American_lobster:T=6706],[&&NHX:S=CARMA-Green_crab:T=6759])[&&NHX:S=Crustacea:T=6657] +,[&&NHX:S=LIMPO-Atlantic_horseshoe_crab:T=6850] +) +)[&&NHX:S=Arthropoda:T=6656], + +([begin of Nematoda] +( +([&&NHX:S=CAEEL:T=6239],[&&NHX:S=CAEBR:T=6238])[&&NHX:S=Rhabditidae:T=6243], +[&&NHX:S=HAECO-Haemonchus_contortus:T=6289] +)[&&NHX:S=Rhabditida:T=6236], +[&&NHX:S=ASCSU-Pig_roundworm:T=6253] +)[&&NHX:S=Nematoda:T=6231] + +)[arthropod/nematode group] + +)[&&NHX:S=Bilateria:T=33213], + +( +([&&NHX:S=ACTEQ-European_sea_anemone:T=6106],[&&NHX:S=ANTEL-Sea_anemone:T=6110])[&&NHX:S=Actiniaria-Sea_anemones:T=6103], +[&&NHX:S=TRICY-Jellyfish:T=6141] +)[&&NHX:S=Cnidaria:T=6073] + + +)[&&NHX:S=Eumetazoa:T=6072], + +( +[&&NHX:S=EPHMU-Muellers_freshwater_sponge:T=6052],[&&NHX:S=GEOCY-Geodia_cydonium:T=6047] +)[&&NHX:S=Porifera-Sponges:T=6040] + +)[&&NHX:S=Metazoa:T=33208], + + + +([begin of Fungi] + +( +([begin of Basidiomycota] +( +([&&NHX:S=LENED-Shiitake_mushroom:T=5353],[&&NHX:S=AGABI-Common_mushroom:T=5341])[&&NHX:S=Agaricales:T=5338], +[&&NHX:S=PHACH-Phanerochaete_chrysosporium:T=5306] +)[&&NHX:S=Hymenomycetes:T=5302], +([&&NHX:S=USTMA-Smut_fungus:T=5270],[&&NHX:S=USTSP-Smut_fungus:T=5271])[&&NHX:S=Ustilago:T=5269] +)[&&NHX:S=Basidiomycota], +([begin of Ascomycota] +( +( +( +([&&NHX:S=YEAST:T=4932],[&&NHX:S=SACKL:T=4934])[&&NHX:S=Saccharomyces:T=4930], +([&&NHX:S=KLULA:T=28985],[&&NHX:S=KLUMA:T=4911])[&&NHX:S=Kluyveromyces:T=4910][, +([&&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] +,[&&NHX:S=YAMOH-Yamadazyma_ohmeri:T=34356]] +)[&&NHX:S=Saccharomycetaceae:T=4893], +( +[&&NHX:S=CANAL:T=5476],[&&NHX:S=CANTR:T=5482][,[&&NHX:S=CANGA-Candida_glabrata:T=5478],[&&NHX:S=CANMA-Candida_maltosa:T=5479], +[&&NHX:S=CANBO-Candida boidinii:T=5477]] +)[&&NHX:S=anamorphic_Saccharomycetales:T=118267] +)[&&NHX:S=Saccharomycetes:T=4891], +( +([&&NHX:S=NEUCR:T=5141],[&&NHX:S=NEUIN:T=5142])[&&NHX:S=Sordariales:T=5139], +([&&NHX:S=ASPNG:T=5061],[&&NHX:S=EMENI:T=5072])[&&NHX:S=Eurotiales:T=5042]) +), +([&&NHX:S=SCHPO:T=4896],[&&NHX:S=PNECA-Pneumocystis_carinii:T=4754]) +)[&&NHX:S=Ascomycota] +), +( +[&&NHX:S=MORPI-Mortierella_alpina:T=64518],[&&NHX:S=MUCRO-Mucor_rouxii:T=29923] +)[&&NHX:S=Zygomycota:T=4825] +)[&&NHX:S=Fungi] +), + +([begin of Viridiplantae] +([begin of Streptophyta] +([begin of Charophyta/Embryophyta group] +([begin of Embryophyta] +([begin of Tracheophyta] +([begin of Spermatophyta] +( +([begin of Magnoliophyta] +([begin of Liliopsida] + +( +([&&NHX:S=MAIZE:T=4577],[&&NHX:S=SORBI-Sorghum_bicolor:T=4558])[&&NHX:S=Panicoideae:T=147369], +( +( +([&&NHX:S=HORVU-Barley:T=4513],[&&NHX:S=WHEAT-Triticum_aestivum:T=4565])[&&NHX:S=Triticeae:T=147389], +[&&NHX:S=AVESA-Oat:T=4498] +)[&&NHX:S=Pooideae:T=147368], +[&&NHX:S=ORYSA-Rice:T=4530] +) +)[&&NHX:S=Poaceae-Grasses:T=4479], + +( +[&&NHX:S=ALLCE-Onion:T=4679],[&&NHX:S=ASPOF-Garden_asparagus:T=4686] +)[&&NHX:S=Asparagales:T=73496] + +)[&&NHX:S=Liliopsida-Monocotyledons:T=4447], + +([begin of eudicotyledons] +(([&&NHX:S=TOBAC-Common_tobacco:T=4097],[&&NHX:S=NICPL-Curled_leaved_tobacco:T=4092])[&&NHX:S=Nicotiana:T=4085], +([&&NHX:S=LYCES-Tomato:T=4081],[&&NHX:S=SOLTU-Potato:T=4113])[&&NHX:S=Solanum:T=4107])[&&NHX:S=Asteridae:T=71274], +( + +([begin of Rosidae] + +( +([&&NHX:S=SOYBN:T=3847],[&&NHX:S=PEA:T=3888][,[&&NHX:S=MEDSA-Alfalfa:T=3879]])[&&NHX:S=Fabales:T=72025], +([&&NHX:S=CUCSA-Cucumber:T=3659],[&&NHX:S=CUCMA-Winter_squash:T=3661])[&&NHX:S=Cucurbitales:T=71239] +)[&&NHX:S=eurosids I:T=91835], + +( +( +([&&NHX:S=BRANA-Rape:T=3708],[&&NHX:S=BRACM-Field_mustard:T=3711])[&&NHX:S=Brassica:T=3705] +,[&&NHX:S=ARATH:T=3702] +)[&&NHX:S=Brassicaceae-Mustard_family:T=3700], +( +([&&NHX:S=CITSI-Citrus_sinensis:T=2711],[&&NHX:S=CITUN-Citrus_unshiu:T=55188])[&&NHX:S=Sapindales:T=41937], +([&&NHX:S=GOSHI-Upland_cotton:T=3635],[&&NHX:S=THECC-Cacao:T=3641])[&&NHX:S=Malvales:T=41938] +) +)[&&NHX:S=eurosids II:T=91836] + +)[&&NHX:S=Rosidae:T=71275], + +( +[&&NHX:S=BETVU-Beet:T=3555],[&&NHX:S=SPIOL-Spinach:T=3562] +)[&&NHX:S=Caryophyllidae:T=71273] + +) +)[&&NHX:S=eudicotyledons:T=71240] +)[&&NHX:S=Magnoliophyta-Flowering_plants:T=3398], + +( +[&&NHX:S=EPHTW-Ephedra_tweediana:T=3390],[&&NHX:S=WELMI-Welwitschia_mirabilis:T=3377] +)[&&NHX:S=Gnetophyta:T=58022] + +)[a suspicious grouping], + +( + +( +( +( +[&&NHX:S=PSEMZ-Douglas_fir:T=3357],[&&NHX:S=PINTH-Japanese_black_pine:T=3350] +)[&&NHX:S=Pinaceae:T=3318], +[&&NHX:S=JUNVI-Red_cedar:T=39584] +)[&&NHX:S=Coniferales:T=3313], +[&&NHX:S=GINBI-Ginkgo_biloba:T=3311] +)[a suspicious grouping], + +([&&NHX:S=ZAMFU-Zamia_furfuracea:T=42329],[&&NHX:S=ZAMFI-Zamia_fischeri:T=34342])[&&NHX:S=Cycadales:T=3297] +)[a suspicious grouping] + +)[&&NHX:S=Spermatophyta-Seed_plants:T=58024], + +[&&NHX:S=EQUAR-Field_horsetail:T=3258] + +)[&&NHX:S=Tracheophyta-Vascular_plants:T=58023], + +([begin of Bryophyta] +[&&NHX:S=CERPU-Ceratodon_purpureus:T=3225],[&&NHX:S=PHYPA-Physcomitrella_patens:T=3218] +)[&&NHX:S=Bryophyta-Mosses:T=3208] + +)[&&NHX:S=Embryophyta-Land_plants:T=3193], + +[&&NHX:S=COLOB-Coleochaete_orbicularis:T=3124] + +)[&&NHX:S=Charophyta_Embryophyta_group:T=131221], + +[&&NHX:S=MESVI-Mesostigma_viride:T=41882] + +)[&&NHX:S=Streptophyta:T=35493], + +([begin of Chlorophyta] +( +[&&NHX:S=VOLCA-Volvox_carteri:T=3067], +([&&NHX:S=CHLEU-Chlamydomonas_eugametos:T=3053],[&&NHX:S=CHLRE-Chlamydomonas_reinhardtii:T=3055])[&&NHX:S=Chlamydomonas:T=3052] +)[&&NHX:S=Chlorophyceae:T=3166], +[&&NHX:S=CHLVU-Chlorella_vulgaris:T=3077] +)[&&NHX:S=Chlorophyta-Green_algae:T=3041] + +)[&&NHX:S=Viridiplantae:T=33090] +), +([&&NHX:S=ACHAM-Achlya_ambisexualis:T=4768],[&&NHX:S=COSCS-Costaria_costata:T=2872])[&&NHX:S=Stramenopiles:T=33634] +), +( +([&&NHX:S=BABBO-Babesia_bovis:T=5865],[&&NHX:S=PLAFA-Plasmodium_falciparum:T=5833]) +,[&&NHX:S=PARTE-Paramecium_tetraurelia:T=5888] +)[&&NHX:S=Alveolata:T=33630] +), +([&&NHX:S=PORPU-Porphyra_purpurea:T=2787],[&&NHX:S=CYACA-Cyanidium_caldarium:T=2771])[&&NHX:S=Rhodophyta-Red_algae:T=2763] +)[&&NHX:S=eukaryote_crown_group:T=33089], +[&&NHX:S=DICDI-Dictyostelium_discoideum:T=44689] +), +[&&NHX:S=ENTHI-Entamoeba_histolytica:T=5759]), +( +([&&NHX:S=TRYBB-Trypanosoma_brucei_brucei:T=5702],[&&NHX:S=LEIMA-Leishmania_major:T=5664]) +,[&&NHX:S=EUGGR-Euglena_gracilis:T=3039])[&&NHX:S=Euglenozoa:T=33682] +), +[&&NHX:S=PHYPO-Physarum_polycephalum:T=5791] +), +([&&NHX:S=GIALA-Giardia_intestinalis:T=5741],[&&NHX:S=SPIVO-Spironucleus_vortens:T=58336])[&&NHX:S=Diplomonadida:T=5738] + +)[&&NHX:S=Eukaryota:T=2759], + +([begin of Archaea] + +([begin of Crenarchaeota] +([&&NHX:S=SULAC-Sulfolobus_acidocaldarius:T=2285],[&&NHX:S=SULSO-Sulfolobus_solfataricus:T=2287])[&&NHX:S=Sulfolobus:T=2284], +[&&NHX:S=AERPE-Aeropyrum_pernix:T=56636] +)[&&NHX:S=Crenarchaeota:T=28889], + +([begin of Euryarchaeota] +( +( +([&&NHX:S=METJA-Methanococcus_jannaschii:T=2190],[&&NHX:S=METVA-Methanococcus_vannielii:T=2187])[&&NHX:S=Methanococcales:T=2182], +( +[&&NHX:S=ARCFU-Archaeoglobus_fulgidus:T=2234], +[&&NHX:S=THEAC-Thermoplasma_acidophilum:T=2303] +) +), +([&&NHX:S=PYRFU-Pyrococcus_furiosus:T=2261],[&&NHX:S=PYRHO-Pyrococcus_horikoshii:T=53953])[&&NHX:S=Thermococcales:T=2258] +), +([&&NHX:S=METTH-Methanobacterium_thermoautotrophicum:T=2166],[&&NHX:S=METFE-Methanothermus_fervidus:T=2180])[&&NHX:S=Methanobacteriales:T=2158] +)[&&NHX:S=Euryarchaeota:T=28890] + +)[&&NHX:S=Archaea:T=2157] + +), + + +([begin of Bacteria] + +([&&NHX:S=AQUAE-Aquifex_aeolicus:T=63363],[&&NHX:S=AQUPY-Aquifex_pyrophilus:T=2714])[&&NHX:S=Aquificales:T=32069], +( +([&&NHX:S=THEMA-Thermotoga_maritima:T=2336],[&&NHX:S=THENE-Thermotoga_neapolitana:T=2337])[&&NHX:S=Thermotogales:T=2419], +( +(([&&NHX:S=THEAQ-Thermus_aquaticus:T=271],[&&NHX:S=THETH-Thermus_thermophilus:T=274])[&&NHX:S=Thermus_group:T=68933], +[&&NHX:S=DEIRA-Deinococcus_radiodurans:T=1299])[&&NHX:S=Thermus/Deinococcus_group:T=1297], + +( + +([begin of Firmicutes-grampositive_bacteria] +([begin of Bacillus/Clostridium_group] +( +( +( +( +[&&NHX:S=BACSU-Bacillus_subtilis:T=1423],[&&NHX:S=BACST-Bacillus_stearothermophilus:T=1422][,[&&NHX:S=BACCO-Bacillus_coagulans:T=1398] +,[&&NHX:S=BACCA-Bacillus_caldotenax:T=1395],[&&NHX:S=BACME-Bacillus megaterium:T=1404]] +)[&&NHX:S=Bacillus:T=1386], +[&&NHX:S=STAAU-Staphylococcus_aureus:T=1280] +)[&&NHX:S=Bacillus/Staphylococcus_group:T=1385], +( +([&&NHX:S=STRMU-Streptococcus_mutans:T=1309],[&&NHX:S=STRPN-Streptococcus_pneumoniae:T=1313])[&&NHX:S=Streptococcus:T=1301], +[&&NHX:S=LACLA-Lactococcus_lactis_lactis:T=1360] +)[&&NHX:S=Streptococcaceae:T=1300] +)[&&NHX:S=Bacillus/Lactobacillus/Streptococcus_group:T=91061], +[&&NHX:S=CLOPA-Clostridium_pasteurianum:T=1501] +),[these paranthesis are -- even more -- questionable] +( +([&&NHX:S=MYCGE-Mycoplasma_genitalium:T=2097],[&&NHX:S=MYCPN-Mycoplasma_pneumoniae:T=2104])[&&NHX:S=Mycoplasmatales:T=2085], +[&&NHX:S=ACHLA-Acholeplasma_laidlawii:T=2148] +)[&&NHX:S=Mollicutes:T=31969] +)[&&NHX:S=Bacillus/Clostridium_group:T=31968], +([begin of Actinobacteria] +( +( +([&&NHX:S=MYCTU-Mycobacterium_tuberculosis:T=1773],[&&NHX:S=MYCBO-Mycobacterium_bovis:T=1765])[&&NHX:S=Mycobacterium_tuberculosis_complex:T=77643], +[&&NHX:S=MYCLE-Mycobacterium_leprae:T=1769] +[,[&&NHX:S=MYCSM-Mycobacterium_smegmatis:T=1772]] +)[&&NHX:S=Mycobacterium:T=1763], +[&&NHX:S=CORGL-Corynebacterium_glutamicum:T=1718] +)[&&NHX:S=Corynebacterineae:T=85007], +[&&NHX:S=PROFR-Propionibacterium_freudenreichii_shermanii:T=1752] +)[&&NHX:S=Actinobacteria:T=1760] +)[&&NHX:S=Firmicutes-grampositive_bacteria:T=1239], + +([begin of group of Cyanobacteria, Proteobacteria, Chlamydiales, Green_sulfur, Spirochaetales ?] +( +( +([&&NHX:S=CHLPN-Chlamydophila_pneumoniae:T=83558],[&&NHX:S=CHLTR-Chlamydia_trachomatis:T=813])[&&NHX:S=Chlamydiales/Verrucomicrobia_group:T=51290], +([&&NHX:S=CHLLI-Chlorobium_limicola:T=1092],[&&NHX:S=CHLVI-Chlorobium_vibrioforme:T=1098])[&&NHX:S=Green_sulfur_bacteria:T=1090] +), +([&&NHX:S=LEPIN-Leptospira_interrogans:T=173],[&&NHX:S=BORBU-Borrelia_burgdorferi:T=139])[&&NHX:S=Spirochaetales:T=136] +), + +([begin of group of Cyanobacteria and Proteobacteria ?] + +([begin of Cyanobacteria] +( +([&&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], +([&&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] +)[&&NHX:S=Chroococcales:T=1118], +[&&NHX:S=ANASP-Anabaena_PCC_7120:T=1174] +[,[&&NHX:S=SPIPL-Spirulina_platensis:T=1156]] +)[&&NHX:S=Cyanobacteria:T=1117], + +([begin of Proteobacteria] + +( +( + +([begin of gamma_subdivision] +( +( +( +[&&NHX:S=SALTY-Salmonella_typhimurium:T=602],[&&NHX:S=ECOLI-Escherichia_coli:T=562][,[&&NHX:S=KLEPN-Klebsiella_pneumoniae:T=573]] +)[&&NHX:S=Enterobacteriaceae:T=91347], +[&&NHX:S=BUCAP-Buchnera_aphidicola:T=98794] +)[&&NHX:S=Enterobacteriaceae_and_related_endosymbionts:T=91347], +[&&NHX:S=HAEIN-Haemophilus_influenzae:T=727] +[,[&&NHX:S=AZOVI-Azotobacter_vinelandii:T=354] +,([&&NHX:S=COXBU-Coxiella_burnetii:T=777],[&&NHX:S=LEGPN-Legionella_pneumophila:T=446])[&&NHX:S=Legionellaceae_group:T=118969]] +),[these paranthesis are -- even more -- questionable] +( +[&&NHX:S=PSEPU-Pseudomonas_putida:T=303],[&&NHX:S=PSEAE-Pseudomonas_aeruginosa:T=287] +)[&&NHX:S=Pseudomonas_group:T=72274] +)[&&NHX:S=gamma_subdivision:T=1236], + +([begin of beta_subdivision] +[&&NHX:S=ALCEU-Alcaligenes_eutrophus:T=510], +([&&NHX:S=NEIME-Neisseria_meningitidis:T=487],[&&NHX:S=NEILA-Neisseria_lactamica:T=486]) +)[&&NHX:S=beta_subdivision:T=28216] + +), + +([begin of alpha_subdivision] +([?] +( +([&&NHX:S=RHOCA-Rhodobacter_capsulatus:T=1061],[&&NHX:S=RHOSH-Rhodobacter_sphaeroides:T=1063])[&&NHX:S=Rhodobacter:T=1060], +[&&NHX:S=PARDE-Paracoccus_denitrificans:T=266] +)[&&NHX:S=Rhodobacter_group:T=31989], + +( +( +([&&NHX:S=RHILE-Rhizobium_leguminosarum:T=384],[&&NHX:S=RHITR-Rhizobium_tropici:T=398])[&&NHX:S=Rhizobium:T=379], +[&&NHX:S=AGRTU-Agrobacterium_tumefaciens:T=362] +)[&&NHX:S=Rhizobiaceae:T=82115], +( +[&&NHX:S=BARBA-Bartonella_bacilliformis:T=774],[&&NHX:S=BARQU-Bartonella_quintana:T=803] +)[&&NHX:S=Bartonellaceae:T=772] +)[&&NHX:S=Rhizobiaceae_group:T=356] +), +( +([&&NHX:S=RICPR-Rickettsia_prowazekii:T=782],[&&NHX:S=RICTY-Rickettsia_typhi:T=785])[&&NHX:S=typhus_group:T=114292], +[&&NHX:S=RICRI-Rickettsia_rickettsii:T=783] +)[&&NHX:S=Rickettsiales:T=766] +)[&&NHX:S=alpha_subdivision:T=28211] +), + +([begin of delta/epsilon_subdivisions] +([&&NHX:S=MYXXA-Myxococcus_xanthus:T=34],[&&NHX:S=DESDE-Desulfovibrio_desulfuricans:T=876])[&&NHX:S=delta_subdivision:T=28221], +([&&NHX:S=CAMCO-Campylobacter_coli:T=195],[&&NHX:S=HELPY-Helicobacter_pylori:T=210])[&&NHX:S=epsilon_subdivision:T=29547] +)[&&NHX:S=delta/epsilon_subdivisions:T=68525] + +)[&&NHX:S=Proteobacteria:T=1224] + +)[group of Cyanobacteria and Proteobacteria ?] + +)[group of Cyanobacteria, Proteobacteria, Chlamydiales, Green_sulfur, Spirochaetales ?] + +) +) +) +)[&&NHX:S=Bacteria:T=2]); + -- 1.7.10.2