From 49b5be407256266072185702b7e2bdd1815c2d0f Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 14 May 2013 04:39:33 +0000 Subject: [PATCH] in progress --- forester/data/tol_147.xml | 1388 ++++++++++++++++++++++++--------------------- 1 file changed, 734 insertions(+), 654 deletions(-) diff --git a/forester/data/tol_147.xml b/forester/data/tol_147.xml index a275c84..19129a2 100644 --- a/forester/data/tol_147.xml +++ b/forester/data/tol_147.xml @@ -1526,30 +1526,47 @@ - 7524 - Hemiptera - order + 33342 + Paraneoptera + infraclass - ACYPI - 7029 - ACYPI - Acyrthosiphon pisum - Pea aphid - species - http://www.agroatlas.ru/content/pests/Acyrthosiphon_pisum/Acyrthosiphon_pisum.jpg + 7524 + Hemiptera + order + + ACYPI + + 7029 + ACYPI + Acyrthosiphon pisum + Pea aphid + species + http://www.agroatlas.ru/content/pests/Acyrthosiphon_pisum/Acyrthosiphon_pisum.jpg + + + + RHOPR + + 13249 + RHOPR + Rhodnius prolixus + Triatomid bug + species + http://upload.wikimedia.org/wikipedia/commons/b/b9/Rhodnius_prolixus.jpg + + - RHOPR - 13249 - RHOPR - Rhodnius prolixus - Triatomid bug - species - http://upload.wikimedia.org/wikipedia/commons/b/b9/Rhodnius_prolixus.jpg + 121224 + PEDHC + Pediculus humanus subsp. corporis + Body louse + subspecies + http://upload.wikimedia.org/wikipedia/commons/thumb/9/92/Body_lice.jpg/436px-Body_lice.jpg @@ -3266,11 +3283,12 @@ - MORVER - 78898 - Mortierella verticillata + 1069443 + MVNXX + Mortierella verticillata NRRL 6337 species + http://www.ual.es/GruposInv/myco-ual/galeria17/mortierella.jpg http://www.diark.org/img/species_pict/Mortierella_verticillata @@ -3444,878 +3462,922 @@ Corticata - Archaeplastida + Plants+HC - - 33090 - Viridiplantae - green plants - kingdom - + Archaeplastida - 3193 - Embryophyta + 33090 + Viridiplantae + green plants + kingdom - 58023 - Tracheophyta + 3193 + Embryophyta - 3398 - Magnoliophyta - flowering plants - Angiospermae + 58023 + Tracheophyta - 71240 - eudicotyledons + 3398 + Magnoliophyta + flowering plants + Angiospermae - 91827 - core eudicotyledons + 71240 + eudicotyledons - 71275 - rosids - subclass + 91827 + core eudicotyledons - fabids & malvids + + 71275 + rosids + subclass + - - 91835 - fabids - + fabids & malvids - Rosales & Cucurbitales & Fabales + + 91835 + fabids + - Rosales & Cucurbitales + Rosales & Cucurbitales & Fabales - - 3745 - Rosaceae - family - + Rosales & Cucurbitales - FRAVE - 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 + 3745 + Rosaceae + family + + FRAVE + + 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 + + + + PRUPE + + 3760 + PRUPE + Prunus persica + Peach + Persica vulgaris + Amygdalus persica + species + http://www.mezhenskyjv.narod.ru/foto_sortov/dokaz.jpg + + - PRUPE + CUCSA - 3760 - PRUPE - Prunus persica - Peach - Persica vulgaris - Amygdalus persica + 3659 + CUCSA + Cucumis sativus + Cucumber species - http://www.mezhenskyjv.narod.ru/foto_sortov/dokaz.jpg - CUCSA - 3659 - CUCSA - Cucumis sativus - Cucumber - species + 3814 + Papilionoideae + subfamily + + SOYBN + + 3847 + SOYBN + Glycine max + cv. Wye + Soybean + Glycine hispida + species + + + + MEDTR + + 3880 + MEDTR + Medicago truncatula + Barrel medic + Medicago tribuloides + species + http://crdp.ac-besancon.fr/flore/FABACEAE/photos/medicago_truncatula_30.jpg + + - 3814 - Papilionoideae - subfamily + 3646 + Malpighiales + order - SOYBN - 3847 - SOYBN - Glycine max - cv. Wye - Soybean - Glycine hispida - species + 3977 + Euphorbiaceae + family + + MANES + + 3983 + MANES + Manihot esculenta + Tapioca + Jatropha manihot + species + http://upload.wikimedia.org/wikipedia/commons/9/99/Iwata_kenichi_cassava.jpg + + + + RICCO + + 3988 + RICCO + Ricinus communis + Castor bean + Ricinus sanguineus + species + http://nmorganics.net/wp-content/uploads/2011/09/castor.jpg + + - MEDTR + POPTR - 3880 - MEDTR - Medicago truncatula - Barrel medic - Medicago tribuloides + 3694 + POPTR + Populus trichocarpa + Western balsam poplar + Populus balsamifera subsp. trichocarpa species - http://crdp.ac-besancon.fr/flore/FABACEAE/photos/medicago_truncatula_30.jpg - 3646 - Malpighiales - order + 91836 + malvids - - 3977 - Euphorbiaceae - family - - - MANES - - 3983 - MANES - Manihot esculenta - Tapioca - Jatropha manihot - species - http://upload.wikimedia.org/wikipedia/commons/9/99/Iwata_kenichi_cassava.jpg - - - - RICCO - - 3988 - RICCO - Ricinus communis - Castor bean - Ricinus sanguineus - species - http://nmorganics.net/wp-content/uploads/2011/09/castor.jpg - - - - - POPTR - - 3694 - POPTR - Populus trichocarpa - Western balsam poplar - Populus balsamifera subsp. trichocarpa - species - - - - - - - 91836 - malvids - - - Brassicales & Sapindales - - - 3699 - Brassicales - order - + Brassicales & Sapindales - 3700 - Brassicaceae - family + 3699 + Brassicales + order - 3701 - Arabidopsis - genus + 3700 + Brassicaceae + family - ARALY - 59689 - ARALY - Arabidopsis lyrata - Lyre-leaved rock-cress - species + 3701 + Arabidopsis + genus + + ARALY + + 59689 + ARALY + Arabidopsis lyrata + Lyre-leaved rock-cress + species + + + + ARATH + + 3702 + ARATH + Arabidopsis thaliana + Mouse-ear cress + species + + - ARATH - 3702 - ARATH - Arabidopsis thaliana - Mouse-ear cress + 98038 + THEHA + Thellungiella halophila + Salt cress species + http://mplant.oxfordjournals.org/content/2/1/3/F1.large.jpg + CARPA - 98038 - THEHA - Thellungiella halophila - Salt cress + 3649 + CARPA + Carica papaya + Papaya species - http://mplant.oxfordjournals.org/content/2/1/3/F1.large.jpg + http://www.biopix.com/photos/jko-carica-papaya-00412.jpg + http://www.texasriviera.com/greenthumbs/papaya10.jpg - CARPA - 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 + + + + CITSI + + 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 + + + EUCGR - 2706 - Citrus - genus + 71139 + EUCGR + Eucalyptus grandis + Flooded gum + species + http://www.calflora.net/losangelesarboretum/images/eucalyptus_grandis.jpg - - CITCLE - - 85681 - Citrus clementina - Citrus clementina hort. ex Tanaka - species - http://palmen-bolschetz.de/images/citrus%20clementine.jpg - - - - CITSI - - 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 - - - - EUCGR - - 71139 - EUCGR - Eucalyptus grandis - Flooded gum - species - http://www.calflora.net/losangelesarboretum/images/eucalyptus_grandis.jpg - - + + + VITVI + + 582304 + VITVI + Vitis vinifera + Grape + species + - VITVI - - 582304 - VITVI - Vitis vinifera - Grape - species - - - - - - 91888 - lamiids - - - 4070 - Solanaceae - family + 91888 + lamiids - 4107 - Solanum - genus + 4070 + Solanaceae + family - 49274 - Lycopersicon - subgenus + 4107 + Solanum + genus - 4081 - SOLLC - Solanum lycopersicum - Tomato - Lycopersicon esculentum - species - http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0905/1214.jpeg + 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://upload.wikimedia.org/wikipedia/commons/b/b8/Currant_tomato.jpg + + - 4084 - SOLPI - Solanum pimpinellifolium - Currant tomato - Lycopersicon pimpinellifolium + 4113 + SOLTU + Solanum tuberosum + Potato species - http://upload.wikimedia.org/wikipedia/commons/b/b8/Currant_tomato.jpg + http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0508/0344.jpeg - 4113 - SOLTU - Solanum tuberosum - Potato + 4097 + TOBAC + Nicotiana tabacum + Common tobacco species - http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0508/0344.jpeg + http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0105/2073.jpeg + MIMGU - 4097 - TOBAC - Nicotiana tabacum - Common tobacco + 4155 + MIMGU + Mimulus guttatus + Yellow monkey flower + Yellow monkey flower species - http://calphotos.berkeley.edu/imgs/512x768/0000_0000/0105/2073.jpeg - - MIMGU - - 4155 - MIMGU - Mimulus guttatus - Yellow monkey flower - Yellow monkey flower - species - - + + + AQUCA + + 218851 + AQUCA + Aquilegia caerulea + E.James + Rocky mountain columbine + Aquilegia coerulea + species + http://content9.eol.org/content/2010/01/01/03/15137_large.jpg + - AQUCA - - 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 + 4479 + Poaceae + grass family + Gramineae + family - 147429 - Andropogoneae - Dumort., 1824 - tribe + 147369 + Panicoideae + Link, 1827 + Centothecoideae + subfamily - SORBI - 4558 - SORBI - Sorghum bicolor - Sorghum - Sorghum vulgare - species + 147429 + Andropogoneae + Dumort., 1824 + tribe + + SORBI + + 4558 + SORBI + Sorghum bicolor + Sorghum + Sorghum vulgare + species + + + + MAIZE + + 4577 + MAIZE + Zea mays + Maize + species + + - MAIZE - 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 + + + + SETIT + + 4555 + SETIT + Setaria italica + Foxtail millet + Panicum italicum + species + http://en.academic.ru/pictures/enwiki/83/Setaria_italica0.jpg + + - 147428 - Paniceae - tribe + 359160 + BEP clade - PANVIR - 38727 - Panicum virgatum - switchgrass - species - http://upload.wikimedia.org/wikipedia/commons/thumb/2/29/PanicumVirgatum.jpg/220px-PanicumVirgatum.jpg - - - - SETIT - - 4555 - SETIT - Setaria italica - Foxtail millet - Panicum italicum - species - http://en.academic.ru/pictures/enwiki/83/Setaria_italica0.jpg + 4527 + Oryza + genus + + ORYSA + + 4530 + ORYSA + Oryza sativa + Rice + species + + + + ORYSJ + + 39947 + ORYSJ + Oryza sativa subsp. japonica + Rice + + - - - - - 359160 - BEP clade - - - - 4527 - Oryza - genus - - ORYSA + BRADI - 4530 - ORYSA - Oryza sativa - Rice + 15368 + BRADI + Brachypodium distachyon + Purple false brome + Trachynia distachya species - - - - ORYSJ - - 39947 - ORYSJ - Oryza sativa subsp. japonica - Rice + http://content5.eol.org/content/2011/01/15/20/16311_large.jpg - - BRADI - - 15368 - BRADI - Brachypodium distachyon - Purple false brome - Trachynia distachya - species - http://content5.eol.org/content/2011/01/15/20/16311_large.jpg - - + + SELMO + + 34167 + SELMO + Selaginella mollis + Moss + species + + - SELMO + PHYPA - 34167 - SELMO - Selaginella mollis + 145481 + PHYPA + Physcomitrella patens subsp. patens Moss - species + subspecies - PHYPA - - 145481 - PHYPA - Physcomitrella patens subsp. patens - Moss - subspecies - - - - - - 3041 - Chlorophyta - phylum - - - 13792 - Mamiellales - order + 3041 + Chlorophyta + phylum - 70447 - Ostreococcus - genus + 13792 + Mamiellales + order - OSTLU - - 436017 - OSTLU - Ostreococcus lucimarinus (strain CCE9901) - - - - OSTRC - 385169 - Ostreococcus sp. RCC809 - species + 70447 + Ostreococcus + genus + + OSTLU + + 436017 + OSTLU + Ostreococcus lucimarinus (strain CCE9901) + + + + OSTRC + + 385169 + Ostreococcus sp. RCC809 + species + + + + OSTTA + + 70448 + OSTTA + Ostreococcus tauri + species + + - OSTTA - 70448 - OSTTA - Ostreococcus tauri - species + 38832 + Micromonas + genus + + MICPC + + 564608 + MICPC + Micromonas pusilla (strain CCMP1545) + Picoplanktonic green alga + + + + MICSR + + 296587 + MICSR + Micromonas sp. (strain RCC299 / NOUM17) + Picoplanktonic green alga + Micromonas sp. RCC299 + species + + - - 38832 - Micromonas - genus - + Trebouxiophyceae & Chlorophyceae - MICPC - 564608 - MICPC - Micromonas pusilla (strain CCMP1545) - Picoplanktonic green alga + 75966 + Trebouxiophyceae + class + + ASTSPC + + 763042 + Asterochloris sp. Cgr/DA1pho + species + http://genome.jgi-psf.org/Astpho1/Figure_3.jpg + + + + CHLSP + + 554065 + Chlorella variabilis + Chlorella sp. NC64A + species + + + + CHLVUL + + 574566 + Coccomyxa sp. C-169 + Chlorella vulgaris C-169 + species + + - MICSR - 296587 - MICSR - Micromonas sp. (strain RCC299 / NOUM17) - Picoplanktonic green alga - Micromonas sp. RCC299 - species + 3042 + Chlamydomonadales + order + + CHLRE + + 3055 + CHLRE + Chlamydomonas reinhardtii + Chlamydomonas smithii + species + + + + VOLCA + + 3067 + VOLCA + Volvox carteri + Green alga + species + + + + + CYAME + + 45157 + CYAME + Cyanidioschyzon merolae + Red alga + species + http://merolae.biol.s.u-tokyo.ac.jp/ + + + + + 2762 + CYAPA + Cyanophora paradoxa + species + http://www.people.vcu.edu/~rfisher/paradoxa.jpg + + + + + + + 55529 + GUITH + Guillardia theta + Cryptomonas phi + species + http://genome.jgi.doe.gov/public/Guith1/Gtheta_SEM.jpg + + + Multiple Gene Phylogenies Support the Monophyly of Cryptomonad and Haptophyte Host Lineages + + + + + + EMIHU + + 2903 + EMIHU + Emiliania huxleyi + species + + + + + + Heterokonta & Alveolata + + + 33630 + Alveolata + + + + 5794 + Apicomplexa + phylum + - Trebouxiophyceae & Chlorophyceae + + 422676 + Aconoidasida + class + - 75966 - Trebouxiophyceae - class + 5820 + Plasmodium + genus - ASTSPC + PLACH - 763042 - Asterochloris sp. Cgr/DA1pho + 5825 + PLACH + Plasmodium chabaudi species - http://genome.jgi-psf.org/Astpho1/Figure_3.jpg - CHLSP + PLAFA - 554065 - Chlorella variabilis - Chlorella sp. NC64A + 5833 + PLAFA + Plasmodium falciparum species - CHLVUL + PLAYO - 574566 - Coccomyxa sp. C-169 - Chlorella vulgaris C-169 - species + 73239 + PLAYO + Plasmodium yoelii yoelii + subspecies + Theileria - 3042 - Chlamydomonadales - order + 5873 + Theileria + genus - CHLRE + THEAN - 3055 - CHLRE - Chlamydomonas reinhardtii - Chlamydomonas smithii + 5874 + THEAN + Theileria annulata species - VOLCA + THEPA - 3067 - VOLCA - Volvox carteri - Green alga + 5875 + THEPA + Theileria parva species - - - - CYAME - - 45157 - CYAME - Cyanidioschyzon merolae - Red alga - species - http://merolae.biol.s.u-tokyo.ac.jp/ - - - - - Chromalveolate - - - - Heterokonta & Alveolata - - - 33630 - Alveolata - - 5794 - Apicomplexa - phylum + 423054 + Eimeriorina + suborder - 422676 - Aconoidasida - class + 5806 + Cryptosporidium + genus + CRYHO - 5820 - Plasmodium - genus + 237895 + CRYHO + Cryptosporidium hominis + species - - PLACH - - 5825 - PLACH - Plasmodium chabaudi - species - - - - PLAFA - - 5833 - PLAFA - Plasmodium falciparum - species - - - - PLAYO - - 73239 - PLAYO - Plasmodium yoelii yoelii - subspecies - - - Theileria + CRYPV - 5873 - Theileria - genus + 5807 + CRYPV + Cryptosporidium parvum + species - - THEAN - - 5874 - THEAN - Theileria annulata - species - - - - THEPA - - 5875 - THEPA - Theileria parva - species - - - - 423054 - Eimeriorina - suborder - + Eimeria & Toxoplasma + + The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees + + + - 5806 - Cryptosporidium - genus + 5802 + EIMTE + Eimeria tenella + Coccidian parasite + species + http://www.k-state.edu/parasitology/625tutorials/FIGtenella.jpg - - CRYHO - - 237895 - CRYHO - Cryptosporidium hominis - species - - - - CRYPV - - 5807 - CRYPV - Cryptosporidium parvum - species - - - Eimeria & Toxoplasma - - The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees - - - - - - 5802 - EIMTE - Eimeria tenella - Coccidian parasite - species - http://www.k-state.edu/parasitology/625tutorials/FIGtenella.jpg - - - - TOXGO - - 5811 - TOXGO - Toxoplasma gondii - species - - + TOXGO + + 5811 + TOXGO + Toxoplasma gondii + species + + + + + 6020 + Oligohymenophorea + class + + PARTE - 6020 - Oligohymenophorea - class + 5888 + PARTE + Paramecium tetraurelia + species + + + + TETTH + + 5911 + TETTH + Tetrahymena thermophila + species - - PARTE - - 5888 - PARTE - Paramecium tetraurelia - species - - - - TETTH - - 5911 - TETTH - Tetrahymena thermophila - species - - + + + + 33634 + Stramenopiles + Patterson 1989, emend. Adl et al. 2005 + Chromophyta + heterokonts + - Heterokonta + Pelagophyceae & Bacillariophyta & Oomycetes - 33634 - stramenopiles - Chromophyta + + Seven Gene Phylogeny of Heterokonts + + + - Pelagophyceae_Bacillariophyta + Pelagophyceae & Bacillariophyta 2836 @@ -4331,12 +4393,13 @@ FRACY - 911694 + 186039 FRACY Fragilariopsis cylindrus Krieger Nitzschia cylindrus species + http://www.awi.de/fileadmin/user_upload/News/Press_Releases/2012/1._Quartal/000_Fragilariposis_Chloroplasten_GDieckmann_w.jpg @@ -4351,20 +4414,19 @@ - THAPS - 916868 + 35128 THAPS Thalassiosira pseudonana Hasle & Heimdal Marine diatom Cyclotella nana species + http://www.genomenewsnetwork.org/gnn_images/sequenced_genomes/thalassiosira_pseudonana.jpg - AURAN 912461 AURAN @@ -4381,17 +4443,17 @@ genus - PHYIN 4787 PHYIN Phytophthora infestans + (Mont.) de Bary 1876 Potato late blight fungus species + http://bioweb.uwlax.edu/bio203/s2007/benrud_jaco/index_files/image4901.jpg - PHYRM 164328 PHYRM @@ -4401,24 +4463,42 @@ - PHYSO 67593 + PHYSO Phytophthora sojae + Soybean stem and root rot agent + Phytophthora megasperma f. sp. glycines species + http://genome.jgi-psf.org/Physo1_1/pramorum.jpg - - - EMIHU - - 2903 - EMIHU - Emiliania huxleyi - species - + + + 33674 + Thraustochytriaceae + Thraustochytriales + family + + + + 702273 + AKEXX + Aplanochytrium kerguelense PBS07 + http://upload.wikimedia.org/wikipedia/commons/thumb/9/91/Aplanolm.jpg/120px-Aplanolm.jpg + + + + + 876976 + SAGXX + Schizochytrium aggregatum ATCC 28209 + http://genome.jgi-psf.org/public/Schag1/120124-ATCC28209-22.JPG + + + -- 1.7.10.2