From 9b96b81b72f2149a88da9ac48301bcd428081d62 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 18 Oct 2012 19:57:52 +0000 Subject: [PATCH] in progress --- forester/data/tol_144.xml | 6392 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 6392 insertions(+) create mode 100644 forester/data/tol_144.xml diff --git a/forester/data/tol_144.xml b/forester/data/tol_144.xml new file mode 100644 index 0000000..7d1141d --- /dev/null +++ b/forester/data/tol_144.xml @@ -0,0 +1,6392 @@ + + + + + cellular_organisms + + + Neomura + + + + 2759 + Eukaryota + superkingdom + + + Unikonta + + Opisthokonta & Apusozoa + + + 33154 + Opisthokonta + Fungi/Metazoa group + + + + Holozoa + + + Choanoflagellatea & Metazoa + + Metazoa + + 33208 + Metazoa + kingdom + + + Eumetazoa + + + + Bilateria_Cnidaria + + Bilateria + + Deuterostomia + + + + Chordata + + 7711 + Chordata + phylum + + + Urochordata & Vertebrata + + + 7742 + Vertebrata + + + + 7776 + Gnathostomata + jawed vertebrates + 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ATCC 50818 + species + + + + + + Ichthyophonida & Filasterea + + + 198625 + Ichthyophonida + order + + + + 4881 + AMOPA + Amoebidium parasiticum + species + http://www.diark.org/img/species_pict/Amoebidium_parasiticum + + + + SPHARC + + 72019 + Sphaeroforma arctica + species + http://www.sciencedirect.com/cache/MiamiImageURL/1-s2.0-S0168952507000236-gr2.jpg + + + + + + Filasterea + + + + + + + CAPOWC + + 192875 + Capsaspora owczarzaki + species + + + + MINVIB + + 134558 + Ministeria vibrans + species + + + + + + + + Holomycota + Nucletmycea + + + + 4751 + Fungi + kingdom + + + Dikarya & Mucoromycotina & Kickxellomycotina & Blastocladiomycota & Chytridiomycota & Neocallimastigomycota + + Dikarya & Mucoromycotina & Kickxellomycotina & Blastocladiomycota & Chytridiomycota + + Dikarya & Mucoromycotina & Kickxellomycotina & Blastocladiomycota + + Dikarya & Mucoromycotina & Kickxellomycotina + + Dikarya & Mucoromycotina + + + 451864 + Dikarya + subkingdom + + + + + + + + 4890 + Ascomycota + phylum + + + Pezizomycotina_Saccharomycetales + + + 147538 + Pezizomycotina + Euascomycota + subphylum + + + A five-gene phylogeny of Pezizomycotina + + + + + + 716546 + Leotiomyceta + + + Sordariomyceta & Dothideomycetes & Trichocomaceae & Lecanoromycetes + + Sordariomyceta & Dothideomycetes & Lecanoromycetes + + Sordariomyceta & Lecanoromycetes + + + 715989 + Sordariomyceta + + + + 147550 + Sordariomycetes + class + + + Magnaporthales & Hypocreales + + + 5125 + Hypocreales + order + + + ACRALC + + 398408 + Acremonium alcalophilum + species + http://genome.jgi-psf.org/public/Acral1_c3a/Acral1.jpg + + + + + 5518 + GIBZE + Gibberella zeae + Wheat head blight fungus + Fusarium graminearum + species + + + + + 29875 + TRIVE + Trichoderma virens + Gliocladium virens + Trichoderma virens + species + + + + + + 148305 + MAGGR + Magnaporthe grisea + Rice blast fungus + Pyricularia grisea + species + + + + + + 5139 + Sordariales + order + + + + 35718 + Chaetomiaceae + family + + + + 35719 + Thielavia + genus + + + MYCTHE + + 573728 + Myceliophthora thermophila + (Apinis) Oorschot 1977 + Sporotrichum thermophilum + anamorph of Thielavia heterothallica + species + http://genome.jgi-psf.org/public/Spoth2/Spoth0.jpg + + + + THITER + + 193532 + Thielavia terrestris + Malloch & Cain 1972 + Acremonium alabamense + species + http://genome.jgi-psf.org/public/Thite2/Thite1.jpg + + + + + + 1029505 + CHAGB + Chaetomium globosum + Kunze 1817 + Soil fungus + species + + + + + + 5141 + NEUCR + Neurospora crassa + species + + + + + + + 147548 + Leotiomycetes + class + + + + 28983 + Sclerotiniaceae + family + + + + 40559 + BOTFU + Botryotinia fuckeliana + Noble rot fungus + Botrytis cinerea + species + + + + + 5180 + SCLSC + Sclerotinia sclerotiorum + White mold + Whetzelinia sclerotiorum + species + + + + + OIDMAI + + 78148 + Oidiodendron maius + species + + + + + + + 388435 + Lecanoromycetidae + subclass + + + CLAGRA + + 27339 + Cladonia grayi + Cladonia grayi Merr + species + http://upload.wikimedia.org/wikipedia/commons/b/b6/Cladonia_grayi-11.jpg + + + + XANPAR + + 107463 + Xanthoria parietina + species + http://upload.wikimedia.org/wikipedia/commons/thumb/7/70/Xanthoria_parietina_%2806_03_31%29.jpg/800px-Xanthoria_parietina_%2806_03_31%29.jpg + + + + + + + 147541 + Dothideomycetes + class + + + A class-wide phylogenetic assessment of Dothideomycetes + + + + 134362 + Capnodiales + order + + + + 41254 + Mycosphaerella + genus + + + MYCFI + + 83344 + Mycosphaerella fijiensis + species + + + + + 54734 + MYCGR + Mycosphaerella graminicola + Speckled leaf blotch fungus + Septoria tritici + species + + + + + 64363 + MYCPJ + Mycosphaerella pini + Red band needle blight disease fungus + Dothistroma septosporum + Dothistroma pini + species + + + + MYCPOP + + 85929 + Mycosphaerella populorum + Septoria musiva + species + + + + + BAUCOM + + 430998 + Baudoinia compniacensis + species + http://www.diark.org/img/species_pict/Baudoinia_compniacensis + + + + + + 715340 + Pleosporineae + suborder + + + + 28556 + Pleosporaceae + family + + + Cochliobolus & Setosphaeria + + + 5015 + Cochliobolus + genus + + + + 5016 + COCHE + Cochliobolus heterostrophus + Drechslera maydis + species + + + + + 45130 + COCSA + Cochliobolus sativus + Bipolaris sorokiniana + species + http://www.plantmanagementnetwork.org/pub/php/diagnosticguide/2003/rootrot/image/mathre6sm.jpg + + + + + + 93612 + SETTU + Setosphaeria turcica + (Luttr.) K.J. Leonard & Suggs, (1974) + Northern corn leaf blight disease fungus + Exserohilum turcicum + Helminthosporium turcicum + species + http://www.pflanzenkrankheiten.ch/diseases/STU/figures_STU/HTU_Mais_Mik_7_k.jpg + http://www.pflanzenkrankheiten.ch/diseases/STU/figures_STU/Exserohilum_turcicum_001_k.jpg + + + + + + 426418 + PYRTR + Pyrenophora tritici-repentis (strain Pt-1C-BFP) + Wheat tan spot fungus + Drechslera tritici-repentis + + + + + + 13684 + PHANO + Phaeosphaeria nodorum + Glume blotch fungus + Septoria nodorum + species + + + + + + + + 28568 + Trichocomaceae + family + + + Neosartorya_Emericella + + + 195546 + EMENI + Emericella nidulans + Vuill. 1927 + Aspergillus nidulans + species + + + + + 331117 + NEOFI + Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) + Aspergillus fischerianus + + + + + + 5052 + Aspergillus + genus + + + + 5059 + ASPFL + Aspergillus flavus + species + + + + + 5061 + ASPNG + Aspergillus niger + species + + + + + + + + 33183 + 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var. bicolor + species + https://www.llnl.gov/news/newsreleases/2006/images/Laccaria_big.jpg + + + + + GYMLUX + + 206324 + Gymnopus luxurians + species + http://www.mushroomexpert.com/images/kuo3/gymnopus_luxurians_02.jpg + + + + + + 5322 + PLEOS + Pleurotus ostreatus + Oyster mushroom + White-rot fungus + species + http://botit.botany.wisc.edu/toms_fungi/images/post1.jpg + + + + + + 68889 + Boletales + Melanogastrales + Sclerodermatales + order + + + + 227334 + Coniophorineae + suborder + + + CONPUT + + 80637 + Coniophora puteana + Schum. ex Fries + cellar fungus + species + http://genome.jgi-psf.org/public/Conpu1/P1240066_dp.jpg + + + + SERLAC + + 85982 + Serpula lacrymans + dry rot fungus + species + http://www.biolib.cz/IMG/GAL/BIG/18135.jpg + + + + + HYDPIN + + 388859 + Hydnomerulius pinastri + Spiny dry rot fungus + species + http://mycoweb-stv.narod.ru/fungi/Submitted/STV1/Hydnomerulius_pinastri_1_STV_20100913.jpg + + + + + + JAAARG + + 202697 + Jaapia argillacea + species + http://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Jaapia-argillacea.jpeg/640px-Jaapia-argillacea.jpeg + + + + + + 104355 + GLOTR + Gloeophyllum trabeum + Brown rot fungus + species + http://www.cbs.knaw.nl/images/Images_CBSFungi/CD/0001/0008/Gloeophyllum_trabeum.jpg + + + + + + 5303 + Aphyllophorales + Gäum. (1926) + Shelf Fungi + Polyporales + order + + + + 83233 + Coriolaceae + family + + + The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes) + + + + + + + Postia & Fomitopsis & Wolfiporia & Trametes + + Antrodia clade + + Antrodia clade + + + FOMPIN + + 40483 + Fomitopsis pinicola + P. Karst. 1881 + Red banded polypore + Fomes pinicola + species + http://content6.eol.org/content/2009/06/07/01/48471_large.jpg + + + + POSPL + + 104341 + Postia placenta + species + http://www.commanster.eu/commanster/Mushrooms/Polypore/SuPolypore/Postia.placenta.jpg + + + + + core polyporoid clade + + core polyporoid clade + + + + 5325 + TRAVE + Trametes versicolor + (L.) Lloyd 1921 + White-rot fungus + Coriolus versicolor + Bjerkandera versicolor + species + http://www.mykoweb.com/CAF/photos/Trametes_versicolor(bab-1).jpg + http://www.mykoweb.com/CAF/photos/Trametes_versicolor(bab-2).jpg + http://www.mykoweb.com/CAF/photos/Trametes_versicolor(mgw-01).jpg + http://genome.jgi-psf.org/public/Trave1/Trametes_versicolor.JPG + + + + WOLCOC + + 81056 + Wolfiporia cocos + species + http://toolate.s7.coreserver.jp/kinoko/fungi/wolfiporia_cocos/w_cocos_002.jpg + + + + + + + 42742 + CERSU + Ceriporiopsis subvermispora + species + + + + + DICSQU + + 114155 + Dichomitus squalens + (P. Karst.) D. A. Reid 1965 + Red rot + Polyporus anceps + species + http://www.fs.fed.us/r3/resources/health/field-guide/images/large/sds-f199-large.jpg + + + + + + + 13563 + HETAN + Heterobasidion annosum + Root rot fungus + species + + + + + + 5215 + Tremellaceae + family + + + + 5207 + CRYNE + Cryptococcus neoformans + Filobasidiella neoformans + species + + + + + 1029985 + TREME + Tremella mesenterica + Pers. 1800 + Jelly fungus + Yellow Brain + Tremella lutescens + species + + + + + + + 452284 + Ustilaginomycotina + subphylum + + + + 425265 + MALGO + Malassezia globosa (strain ATCC MYA-4612 / CBS 7966) + Dandruff-associated fungus + + + + + 5270 + USTMA + Ustilago maydis + Smut fungus + species + + + + + + + 29000 + Pucciniomycotina + subphylum + + + + 5258 + Pucciniales + rusts + order + + + + 156696 + MELLP + Melampsora laricis-populina + Kleb. 1902 + Melampsora larici-populina + Melampsora laricipopulina + species + + + + + 1029947 + PUCGR + Puccinia graminis + Pers. 1794 + Black stem rust fungus + Wheat rust + species + + + + + + 89013 + mitosporic Sporidiobolales + + + + 29898 + RHOGR + Rhodotorula graminis + Yeast + species + + + + SPORO + + 1013696 + Sporobolomyces roseus + Kluyver & C. B. Niel 1924 + species + + + + + + + + 148960 + WALSE + Wallemia sebi + species + + + + + + + 451507 + Mucoromycotina + subphylum + + + + 34489 + Mucoraceae + family + + + + 36080 + MUCCI + Mucor circinelloides + Mucor griseo-roseus + species + + + + + 4837 + PHYBL + Phycomyces blakesleeanus + species + + + + + 64495 + RHIOR + Rhizopus oryzae + Rhizopus delemar + species + + + + + MORVER + + 78898 + Mortierella verticillata + species + http://www.diark.org/img/species_pict/Mortierella_verticillata + + + + + + COEREV + + 61392 + Coemansia reversa + species + + + + + + 28583 + ALLMA + Allomyces macrogynus + species + + + + + + 4761 + Chytridiomycota + chytrids + Mastigomycotina + phylum + + + + 451435 + Chytridiomycetes + class + + + + 109871 + BATDE + Batrachochytrium dendrobatidis + Frog chytrid fungus + species + + + + + 109760 + SPIPN + Spizellomyces punctatus + species + + + + + GONPRO + + 157984 + Gonapodya prolifera + A. Fisch. 1892 + species + http://genome.jgi-psf.org/public/Ganpr1/Picture5.jpg + + + + + + PIRSPE + + 73868 + Piromyces sp. E2 + species + http://www.bsu.edu/classes/ruch/msa/barr/4-17.jpg + + + + + + 6035 + ENCCU + Encephalitozoon cuniculi + Microsporidian parasite + species + + + + + Fonticula & Nucleariidae + + + + FONALB + + 691883 + Fonticula alba + Fonticula alba Worley, Raper & Hohl. 1979 + species + + + + NUCSIM + + 154970 + Nuclearia simplex + species + + + + + + + THETRA + + 529818 + Thecamonas trahens + species + + + + + Amoebozoa + + 554915 + Amoebozoa + + + Dictyostelium + + 5782 + Dictyostelium + genus + + + + 44689 + DICDI + Dictyostelium discoideum + Slime mold + species + + + + + 5786 + DICPU + Dictyostelium purpureum + Slime mold + species + + + + + + 5759 + ENTHI + Entamoeba histolytica + species + + + + + + Bikonta + + + + Corticata + + Archaeplastida + + + 33090 + Viridiplantae + green plants + kingdom + + + + 3193 + Embryophyta + + + + 58023 + Tracheophyta + + + + 3398 + Magnoliophyta + flowering plants + Angiospermae + + + + 71240 + eudicotyledons + + + + 91827 + core eudicotyledons + + + + 71275 + rosids + subclass + + + fabids & malvids + + + 91835 + fabids + + + Rosales & Cucurbitales & Fabales + + Rosales & Cucurbitales + + + 3745 + Rosaceae + family + + + + 57918 + FRAVE + Fragaria vesca + Woodland strawberry + Fragaria vesca L. + European strawberry + alpine strawberry + species + http://www.boga.ruhr-uni-bochum.de/html/Fragaria.vesca.ja6.jpg + http://caliban.mpiz-koeln.mpg.de/thome/band3/tafel_092_small.jpg + + + + + 3760 + PRUPE + Prunus persica + Peach + Persica vulgaris + Amygdalus persica + species + http://www.mezhenskyjv.narod.ru/foto_sortov/dokaz.jpg + + + + + + 3659 + CUCSA + Cucumis sativus + Cucumber + species + + + + + + 3814 + Papilionoideae + subfamily + + + + 3847 + SOYBN + Glycine max + cv. Wye + Soybean + Glycine hispida + species + + + + + 3880 + MEDTR + Medicago truncatula + Barrel medic + Medicago tribuloides + species + http://crdp.ac-besancon.fr/flore/FABACEAE/photos/medicago_truncatula_30.jpg + + + + + + + 3646 + Malpighiales + order + + + + 3977 + Euphorbiaceae + family + + + + 3983 + MANES + Manihot esculenta + Tapioca + Jatropha manihot + species + http://upload.wikimedia.org/wikipedia/commons/9/99/Iwata_kenichi_cassava.jpg + + + + + 3988 + RICCO + Ricinus communis + Castor bean + Ricinus sanguineus + species + http://nmorganics.net/wp-content/uploads/2011/09/castor.jpg + + + + + + 3694 + POPTR + Populus trichocarpa + Western balsam poplar + Populus balsamifera subsp. trichocarpa + species + + + + + + + 91836 + malvids + + + Brassicales & Sapindales + + + 3699 + Brassicales + order + + + + 3700 + Brassicaceae + family + + + + 3701 + Arabidopsis + genus + + + + 59689 + ARALY + Arabidopsis lyrata + Lyre-leaved rock-cress + species + + + + + 3702 + ARATH + Arabidopsis thaliana + Mouse-ear cress + species + + + + + + 98038 + THEHA + Thellungiella halophila + Salt cress + species + http://thellungiella.org/images/thellun1.jpg + + + + + + 3649 + CARPA + Carica papaya + Papaya + species + http://www.biopix.com/photos/jko-carica-papaya-00412.jpg + http://www.texasriviera.com/greenthumbs/papaya10.jpg + + + + + + 2706 + Citrus + genus + + + CITCLE + + 85681 + Citrus clementina + Citrus clementina hort. ex Tanaka + species + http://palmen-bolschetz.de/images/citrus%20clementine.jpg + + + + + 2711 + CITSI + Citrus sinensis + Sweet orange + Citrus x sinensis + Citrus aurantium var. sinensis + species + http://www.west-crete.com/flowers/photos/citrus_sinensis-1.jpg + + + + + + + 71139 + EUCGR + Eucalyptus grandis + Flooded gum + species + http://www.calflora.net/losangelesarboretum/images/eucalyptus_grandis.jpg + http://www.anbg.gov.au/projects/eucalypts/images/eucalyptus-grandis-bark.jpg + + + + + + + 582304 + VITVI + Vitis vinifera + Grape + species + + + + + + 91888 + lamiids + + + + 4070 + Solanaceae + family + + + + 4107 + Solanum + genus + + + + 49274 + Lycopersicon + subgenus + + + + 4081 + SOLLC + Solanum lycopersicum + Tomato + Lycopersicon esculentum + species + http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0905/1214.jpeg + + + + + 4084 + SOLPI + Solanum pimpinellifolium + Currant tomato + Lycopersicon pimpinellifolium + species + http://botany.csdl.tamu.edu/FLORA/hdwimages2/hdwt4-14.jpg + + + + + + uniprot + SOLTU + Solanum tuberosum + Potato + species + http://www.hear.org/starr/images/images/plants/600/starr-080914-9947.jpg + + + + + + 4097 + TOBAC + Nicotiana tabacum + Common tobacco + species + http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0105/2073.jpeg + + + + + + 4155 + MIMGU + Mimulus guttatus + Yellow monkey flower + Yellow monkey flower + species + + + + + + + 218851 + AQUCA + Aquilegia caerulea + E.James + Rocky mountain columbine + Aquilegia coerulea + species + http://content9.eol.org/content/2010/01/01/03/15137_large.jpg + + + + + + 4479 + Poaceae + grass family + Gramineae + family + + + + 147369 + Panicoideae + Link, 1827 + Centothecoideae + subfamily + + + + 147429 + Andropogoneae + Dumort., 1824 + tribe + + + + 4558 + SORBI + Sorghum bicolor + Sorghum + Sorghum vulgare + species + + + + + 4577 + MAIZE + Zea mays + Maize + species + + + + + + 147428 + Paniceae + tribe + + + PANVIR + + 38727 + Panicum virgatum + switchgrass + species + http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/PanicumVirgatum.jpg/220px-PanicumVirgatum.jpg + + + + + 4555 + SETIT + Setaria italica + Foxtail millet + Panicum italicum + species + http://en.academic.ru/pictures/enwiki/83/Setaria_italica0.jpg + + + + + + + 359160 + BEP clade + + + + 4527 + Oryza + genus + + + + 4530 + ORYSA + Oryza sativa + Rice + species + + + + + 39947 + ORYSJ + Oryza sativa subsp. japonica + Rice + + + + + + 15368 + BRADI + Brachypodium distachyon + Purple false brome + Trachynia distachya + species + http://content5.eol.org/content/2011/01/15/20/16311_large.jpg + + + + + + + + 34167 + SELMO + Selaginella mollis + Moss + species + + + + + + 145481 + PHYPA + Physcomitrella patens subsp. patens + Moss + subspecies + + + + + + 3041 + Chlorophyta + phylum + + + + 13792 + Mamiellales + order + + + + 70447 + Ostreococcus + genus + + + + 436017 + OSTLU + Ostreococcus lucimarinus (strain CCE9901) + + + + OSTRC + + 385169 + Ostreococcus sp. 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