From 8cc83c3892ebaaf1f362144eabaf01ac0d88b2e9 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 1 Mar 2012 03:10:07 +0000 Subject: [PATCH] in progress --- .../{tol_138.xml => tol_139.xml} | 637 +++++++++++--------- 1 file changed, 344 insertions(+), 293 deletions(-) rename forester/aptx/aptx_example_files/{tol_138.xml => tol_139.xml} (92%) diff --git a/forester/aptx/aptx_example_files/tol_138.xml b/forester/aptx/aptx_example_files/tol_139.xml similarity index 92% rename from forester/aptx/aptx_example_files/tol_138.xml rename to forester/aptx/aptx_example_files/tol_139.xml index 97d3564..8975763 100644 --- a/forester/aptx/aptx_example_files/tol_138.xml +++ b/forester/aptx/aptx_example_files/tol_139.xml @@ -93,10 +93,6 @@ The new framework for understanding placental mammal evolution - - - - Boreoeutheria @@ -168,7 +164,6 @@ Human species http://www.thehindu.com/multimedia/dynamic/00029/IN05_DARWIN_29896f.jpg - http://upload.wikimedia.org/wikipedia/commons/thumb/e/e5/Steve_Jobs_WWDC07.jpg/170px-Steve_Jobs_WWDC07.jpg @@ -1735,327 +1730,428 @@ 147538 Pezizomycotina + Euascomycota subphylum + + A five-gene phylogeny of Pezizomycotina + + + - Sordariomycetes & Leotiomycetes & Dothideomycetes & Eurotiales + + 716546 + Leotiomyceta + - Sordariomycetes & Leotiomycetes & Dothideomycetes + Sordariomyceta & Dothideomycetes & Trichocomaceae & Lecanoromycetes + + - - 147541 - Dothideomycetes - class - - - A class-wide phylogenetic assessment of Dothideomycetes - + Sordariomyceta & Dothideomycetes & Lecanoromycetes - 134362 - Capnodiales - order + 147541 + Dothideomycetes + class + + A class-wide phylogenetic assessment of Dothideomycetes + - 41254 - Mycosphaerella - genus + 134362 + Capnodiales + order - MYCFI - 83344 - Mycosphaerella fijiensis - species - - - - MYCGR - - 54734 - MYCGR - Mycosphaerella graminicola - Speckled leaf blotch fungus - Septoria tritici - species - - - - MYCPOP - - 85929 - Mycosphaerella populorum - Septoria musiva - species + 41254 + Mycosphaerella + genus + + MYCFI + + 83344 + Mycosphaerella fijiensis + species + + + + MYCGR + + 54734 + MYCGR + Mycosphaerella graminicola + Speckled leaf blotch fungus + Septoria tritici + species + + + + MYCPOP + + 85929 + Mycosphaerella populorum + Septoria musiva + species + + + + MYCPJ + + 64363 + MYCPJ + Mycosphaerella pini + Red band needle blight disease fungus + Dothistroma septosporum + Dothistroma pini + species + + - MYCPJ - 64363 - MYCPJ - Mycosphaerella pini - Red band needle blight disease fungus - Dothistroma septosporum - Dothistroma pini + 430998 + BAUCOM + Baudoinia compniacensis species + http://www.diark.org/img/species_pict/Baudoinia_compniacensis - 430998 - BAUCOM - Baudoinia compniacensis - species - http://www.diark.org/img/species_pict/Baudoinia_compniacensis - - - - - - 715340 - Pleosporineae - suborder - - - - 28556 - Pleosporaceae - family + 715340 + Pleosporineae + suborder - Cochliobolus & Setosphaeria + + 28556 + Pleosporaceae + family + - - 5015 - Cochliobolus - genus - + Cochliobolus & Setosphaeria - COCHE - 5016 - COCHE - Cochliobolus heterostrophus - Drechslera maydis - species + 5015 + Cochliobolus + genus + + COCHE + + 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 + + - 45130 - COCSA - Cochliobolus sativus - Bipolaris sorokiniana + 93612 + SETTU + Setosphaeria turcica + (Luttr.) K.J. Leonard & Suggs, (1974) + Northern corn leaf blight disease fungus + Exserohilum turcicum + Helminthosporium turcicum species - http://www.plantmanagementnetwork.org/pub/php/diagnosticguide/2003/rootrot/image/mathre6sm.jpg + 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 + PYRTR - 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 - PYRTR + PHANO - 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 - - PHANO - - 13684 - PHANO - Phaeosphaeria nodorum - Glume blotch fungus - Septoria nodorum - species - - - - - Sordariomycetes & Leotiomycetes - - 147550 - Sordariomycetes - class - + Sordariomyceta & Lecanoromycetes - Magnaporthales & Hypocreales + + 715989 + Sordariomyceta + - 5125 - Hypocreales - order + 147550 + Sordariomycetes + class - TRIVE - - 29875 - TRIVE - Trichoderma virens - Gliocladium virens - Trichoderma virens - species - - - - GIBZE - - 5518 - GIBZE - Gibberella zeae - Wheat head blight fungus - Fusarium graminearum - species - + Magnaporthales & Hypocreales + + + 5125 + Hypocreales + order + + + TRIVE + + 29875 + TRIVE + Trichoderma virens + Gliocladium virens + Trichoderma virens + species + + + + GIBZE + + 5518 + GIBZE + Gibberella zeae + Wheat head blight fungus + Fusarium graminearum + species + + + + ACRALC + + 398408 + Acremonium alcalophilum + species + http://genome.jgi-psf.org/public/Acral1_c3a/Acral1.jpg + + + + + MAGGR + + 148305 + MAGGR + Magnaporthe grisea + Rice blast fungus + Pyricularia grisea + species + + - ACRALC - 398408 - Acremonium alcalophilum - species - http://genome.jgi-psf.org/public/Acral1_c3a/Acral1.jpg + 5139 + Sordariales + order + + + 35718 + Chaetomiaceae + family + + + + 35719 + Thielavia + genus + + + THITER + + 193532 + Thielavia terrestris + Malloch & Cain 1972 + Acremonium alabamense + species + http://genome.jgi-psf.org/public/Thite2/Thite1.jpg + + + + MYCTHE + + 573728 + Myceliophthora thermophila + (Apinis) Oorschot 1977 + Sporotrichum thermophilum + anamorph of Thielavia heterothallica + species + http://genome.jgi-psf.org/public/Spoth2/Spoth0.jpg + + + + + CHAGB + + 1029505 + CHAGB + Chaetomium globosum + Kunze 1817 + Soil fungus + species + + + + + NEUCR + + 5141 + NEUCR + Neurospora crassa + species + + - MAGGR - - 148305 - MAGGR - Magnaporthe grisea - Rice blast fungus - Pyricularia grisea - species - - - - - - 5139 - Sordariales - order - - - 35718 - Chaetomiaceae - family + 147548 + Leotiomycetes + class - 35719 - Thielavia - genus + 28983 + Sclerotiniaceae + family - THITER - 193532 - Thielavia terrestris - Malloch & Cain 1972 - Acremonium alabamense + 40559 + BOTFU + Botryotinia fuckeliana + Noble rot fungus + Botrytis cinerea species - http://genome.jgi-psf.org/public/Thite2/Thite1.jpg - MYCTHE - 573728 - Myceliophthora thermophila - (Apinis) Oorschot 1977 - Sporotrichum thermophilum - anamorph of Thielavia heterothallica + 5180 + SCLSC + Sclerotinia sclerotiorum + White mold + Whetzelinia sclerotiorum species - http://genome.jgi-psf.org/public/Spoth2/Spoth0.jpg - CHAGB + OIDMAI - 1029505 - CHAGB - Chaetomium globosum - Kunze 1817 - Soil fungus + 78148 + Oidiodendron maius species - - NEUCR - - 5141 - NEUCR - Neurospora crassa - species - - - - - - 147548 - Leotiomycetes - class - - 28983 - Sclerotiniaceae - family + 388435 + Lecanoromycetidae + subclass - 40559 - BOTFU - Botryotinia fuckeliana - Noble rot fungus - Botrytis cinerea + 27339 + CLAGRA + Cladonia grayi + Cladonia grayi Merr species + http://upload.wikimedia.org/wikipedia/commons/b/b6/Cladonia_grayi-11.jpg - 5180 - SCLSC - Sclerotinia sclerotiorum - White mold - Whetzelinia sclerotiorum + 107463 + XANPAR + 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 + + + + + 28568 + Trichocomaceae + family + + + Neosartorya_Emericella + + NEOFI + + 331117 + NEOFI + Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) + Aspergillus fischerianus + + - OIDMAI + EMENI - 78148 - Oidiodendron maius + 195546 + EMENI + Emericella nidulans + Vuill. 1927 + Aspergillus nidulans + species + + + + + + 5052 + Aspergillus + genus + + + ASPFL + + 5059 + ASPFL + Aspergillus flavus + species + + + + ASPNG + + 5061 + ASPNG + Aspergillus niger species @@ -2064,84 +2160,39 @@ - 28568 - Trichocomaceae - family + 33183 + Onygenales + order - Neosartorya_Emericella - - NEOFI - - 331117 - NEOFI - Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) - Aspergillus fischerianus - - - - EMENI - - 195546 - EMENI - Emericella nidulans - Vuill. 1927 - Aspergillus nidulans - species - - + COCIM + + 5501 + COCIM + Coccidioides immitis + Valley fever fungus + species + + UNCRE - 5052 - Aspergillus - genus + 336963 + UNCRE + Uncinocarpus reesii (strain UAMH 1704) - - ASPFL - - 5059 - ASPFL - Aspergillus flavus - species - - - - ASPNG - - 5061 - ASPNG - Aspergillus niger - species - - - 33183 - Onygenales - order + 656061 + TUBMM + Tuber melanosporum (strain Mel28) + Perigord black truffle + Tuber melanosporum Mel28 + http://www.gmvmonza.org/images%20parco/Tuber%20melanosporum%20p106.jpg - - COCIM - - 5501 - COCIM - Coccidioides immitis - Valley fever fungus - species - - - - UNCRE - - 336963 - UNCRE - Uncinocarpus reesii (strain UAMH 1704) - - -- 1.7.10.2