Test results for PMGmap and OGdraw
We tested PMGmap with two datasets. Dataset 1 contains 387 mitochondrial genomes obtained on May 23, 2023. All these mitogenomes had only one chromosome. In contrast, Dataset 2 contains 18 mitochondrial genomes obtained on May 23, 2023. All these mitogenomes had more than one chromosomes.
The input files, intermediate files and the output files are presented species by species. For each species, the following five folders are provided. The contents of these folders are described below.
01.Input data before processing contains raw input data downloaded from GenBank
02.Input data after processing contains the GenBank file(s) obtained after PMGmap Preprocess
03.result01 contains the results for PMGmap run with the following parameters:
Interval_ratio of genome map=1,
Scattered repeat sequence threshold=5000,
Ratio of cis-trans splicing genes map=0.02,
Whether choose to draw exons or not=Yes,
Ratio of cis-trans splicing genes map=0.02,
whether choose to draw exons or not= yes,
Whether to draw the shadow or not=Yes.
04.result02: contains the results for PMGmap run with the following parameters:
Interval_ratio of genome map=1,
Scattered repeat sequence threshold=5000,
Ratio of cis-trans splicing genes map=0.02,
Whether choose to draw exons or not=Yes,
Ratio of cis-trans splicing genes map=0.02,
whether choose to draw exons or not= yes,
Whether to draw the shadow or not=Yes.
05.result03: contains the results for PMGmap run with the following parameters:
Interval_ratio of genome map=1,
Scattered repeat sequence threshold=5000,
Ratio of cis-trans splicing genes map=0.02,
Whether choose to draw exons or not=Yes,
Ratio of cis-trans splicing genes map=0.02,
whether choose to draw exons or not= yes,
Whether to draw the shadow or not=Yes.
Lastly, the results run by OGDraw are also provided so they can be compared with those produced with PMGmap.
Last updated: 2023/10/11
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| Abies koreana |
| Acacia ligulata |
| Aconitum kusnezoffii |
| Actinidia chinensis |
| Actinidia latifolia |
| Aegiceras corniculatum |
| Aegilops speltoides var. ligustica |
| Aeginetia indica |
| Ageratum conyzoides |
| Agrostemma githago |
| Ajuga reptans |
| Allardia glabra |
| Allium cepa |
| Ammopiptanthus mongolicus |
| Ammopiptanthus nanus |
| Andreaea regularis |
| Andreaea wangiana |
| Aneura pinguis |
| Anomodon rugelii |
| Anthoceros agrestis |
| Anthoceros angustus |
| Anthoceros punctatus |
| Apium graveolens |
| Aquilaria sinensis |
| Arabidopsis thaliana |
| Arctium lappa |
| Arctium tomentosum |
| Artemisia giraldii |
| Asclepias syriaca |
| Asparagus officinalis |
| Atrichum angustatum |
| Aulacomnium turgidum |
| Bartramia patens |
| Bartramia pomiformis |
| Batis maritima |
| Beta macrocarpa |
| Beta vulgaris subsp. maritima |
| Beta vulgaris subsp. vulgaris |
| Bidens bipinnata |
| Bidens biternata |
| Bidens parviflora |
| Bidens pilosa |
| Bidens tripartita |
| Boechera stricta |
| Bombax ceiba |
| Bougainvillea spectabilis |
| Brachythecium rivulare |
| Brassica carinata |
| Brassica juncea |
| Brassica napus |
| Brassica nigra |
| Brassica oleracea |
| Brassica rapa |
| Brassica rapa subsp. oleifera |
| Bruguiera sexangula |
| Bruguiera x rhynchopetala |
| Bucklandiella orthotrichacea |
| Bupleurum falcatum |
| Butomus umbellatus |
| Buxbaumia aphylla |
| Callicladium imponens |
| Calypogeia arguta |
| Calypogeia fissa subsp. neogaea |
| Calypogeia integristipula |
| Calypogeia neesiana |
| Calypogeia suecica |
| Calystegia soldanella |
| Camellia nitidissima |
| Camellia sinensis |
| Cannabis sativa |
| Capsella rubella |
| Capsicum annuum |
| Carallia brachiata |
| Carex breviculmis |
| Carica papaya |
| Carthamus tinctorius |
| Castilleja paramensis |
| Chenopodium quinoa |
| Chionoloma tenuirostre |
| Chorisodontium aciphyllum |
| Chrysanthemum boreale |
| Chrysopogon zizanioides |
| Cichorium intybus |
| Citrullus lanatus |
| Citrus maxima |
| Citrus sinensis |
| Citrus unshiu |
| Climacium americanum |
| Climacium dendroides |
| Cocos nucifera |
| Codonopsis lanceolata |
| Codriophorus aciculare |
| Corchorus capsularis |
| Corchorus olitorius |
| Cotinus coggygria |
| Cucurbita pepo |
| Cuscuta japonica |
| Cycas taitungensis |
| Cyperus esculentus |
| Daucus carota subsp. sativus |
| Dilutineuron laevigatum |
| Diospyros oleifera |
| Diplophyllum taxifolium |
| Diplostephium hartwegii |
| Dorcoceras hygrometricum |
| Douinia plicata |
| Dracocephalum moldavica |
| Dumortiera hirsuta |
| Eleusine indica |
| Epirixanthes elongata |
| Erythranthe guttata |
| Eucalyptus grandis |
| Euonymus alatus |
| Evolvulus alsinoides |
| Fagus sylvatica |
| Fossombronia foveolata |
| Fragaria gracilis |
| Fragaria iinumae |
| Fragaria iturupensis |
| Fragaria mandshurica |
| Fragaria moschata |
| Fragaria nilgerrensis |
| Fragaria nubicola |
| Fragaria orientalis |
| Fragaria pentaphylla |
| Fragaria tibetica |
| Fragaria vesca |
| Fragaria viridis |
| Fragaria x ananassa |
| Frisvollia varia |
| Funaria hygrometrica |
| Geranium maderense |
| Geum urbanum |
| Ginkgo biloba |
| Gleditsia sinensis |
| Glycine max |
| Glycine soja |
| Glycyrrhiza uralensis |
| Gossypium arboreum |
| Gossypium barbadense |
| Gossypium davidsonii |
| Gossypium harknessii |
| Gossypium hirsutum |
| Gossypium raimondii |
| Gossypium thurberi |
| Gossypium trilobum |
| Gymnomitrion concinnatum |
| Haematoxylum brasiletto |
| Haplomitrium hookeri |
| Helianthus annuus |
| Helianthus grosseserratus |
| Helianthus neglectus |
| Helianthus occidentalis |
| Helianthus strumosus |
| Helianthus tuberosus |
| Helicanthes elasticus |
| Hepatica maxima |
| Hernandia nymphaeifolia |
| Hesperelaea palmeri |
| Hibiscus cannabinus |
| Hyoscyamus niger |
| Ilex pubescens |
| Ipomoea batatas |
| Ipomoea nil |
| Jasminum sambac |
| Juncus effusus |
| Kandelia obovata |
| Lactuca saligna |
| Lactuca sativa |
| Lagerstroemia indica |
| Leiosporoceros dussii |
| Leucaena trichandra |
| Lewinskya speciosa |
| Libidibia coriaria |
| Liriodendron tulipifera |
| Lotus japonicus |
| Luffa acutangula |
| Luzula sylvatica |
| Macadamia integrifolia |
| Magnolia biondii |
| Malania oleifera |
| Malus baccata |
| Malus domestica |
| Malus sieversii |
| Malus sylvestris |
| Mangifera longipes |
| Manihot esculenta |
| Marchantia paleacea |
| Marchantia polymorpha subsp. ruderalis |
| Medicago sativa |
| Medicago truncatula |
| Melastoma dodecandrum |
| Melastoma sanguineum |
| Melicope pteleifolia |
| Metzgeria furcata |
| Mielichhoferia elongata |
| Mirabilis himalaica |
| Mirabilis jalapa |
| Morus notabilis |
| Myurella julacea |
| Nelumbo nucifera |
| Nepenthes x ventrata |
| Nicotiana attenuata |
| Nicotiana tabacum |
| Niphotrichum elongatum |
| Niphotrichum ericoides |
| Nothoceros aenigmaticus |
| Nowellia curvifolia |
| Nymphaea colorata |
| Nymphaea hybrid cultivar |
| Ophioglossum californicum |
| Ophioglossum vulgatum |
| Ormosia boluoensis |
| Orthotrichum bicolor |
| Orthotrichum callistomum |
| Orthotrichum diaphanum |
| Orthotrichum gymnostomum |
| Orthotrichum macrocephalum |
| Orthotrichum obtusifolium |
| Orthotrichum stellatum |
| Oryza minuta |
| Oryza rufipogon |
| Oryza sativa |
| Oryza sativa Indica Group |
| Oryza sativa Japonica Group |
| Osmanthus didymopetalus |
| Osmanthus fragrans |
| Paeonia lactiflora |
| Panax quinquefolius |
| Passiflora edulis |
| Pereskia aculeata |
| Phaeoceros laevis |
| Phaseolus vulgaris |
| Phlegmariurus squarrosus |
| Phoenix dactylifera |
| Phoenix roebelenii |
| Photinia serratifolia |
| Phyllolobium chinense |
| Physcomitrium patens |
| Physochlaina orientalis |
| Pinus taeda |
| Pisum abyssinicum |
| Pisum fulvum |
| Planicladium nitidulum |
| Platostoma chinense |
| Platycodon grandiflorus |
| Plenogemma phyllantha |
| Pleurozia purpurea |
| Pohlia nutans |
| Polytrichum commune |
| Pongamia pinnata |
| Populus alba |
| Populus davidiana |
| Populus tremula |
| Populus tremula x Populus alba |
| Porella platyphylla |
| Potentilla micrantha |
| Prunus armeniaca |
| Prunus avium |
| Prunus kanzakura |
| Prunus mira |
| Prunus mume |
| Prunus salicina |
| Prunus salicina x Prunus armeniaca |
| Prunus schneideriana |
| Prunus sibirica |
| Prunus yedoensis |
| Pseudanomodon attenuatus |
| Psychotria serpens |
| Psychotria viridis |
| Ptilidium ciliare |
| Ptychomnion cygnisetum |
| Pulsatilla cernua |
| Pulsatilla chinensis |
| Pulsatilla dahurica |
| Punica granatum |
| Pyrus betulifolia |
| Pyrus communis |
| Pyrus ussuriensis x Pyrus communis |
| Pyrus x bretschneideri |
| Racomitrium emersum |
| Racomitrium lanuginosum |
| Raphanus sativus |
| Rhaphiolepis bibas |
| Rhazya stricta |
| Rhodiola crenulata |
| Rhodiola tangutica |
| Rhododendron simsii |
| Rhododendron x pulchrum |
| Rhodomyrtus tomentosa |
| Rhynchospora breviuscula |
| Rhynchospora pubera |
| Rhynchospora tenuis |
| Riccia fluitans |
| Rosa chinensis |
| Rosa rugosa |
| Rotheca serrata |
| Rubus chingii |
| Salix brachista |
| Salix cardiophylla |
| Salix dunnii |
| Salix integra |
| Salix koriyanagi |
| Salix paraflabellaris |
| Salix polaris |
| Salix purpurea |
| Salix suchowensis |
| Salix triandra |
| Salix wilsonii |
| Salvia miltiorrhiza |
| Sanionia uncinata |
| Sapindus mukorossi |
| Saposhnikovia divaricata |
| Saussurea costus |
| Saussurea inversa |
| Scapania ampliata |
| Schisandra sphenanthera |
| Scyphiphora hydrophyllacea |
| Sedum plumbizincicola |
| Senna occidentalis |
| Senna tora |
| Silene latifolia |
| Sinapis arvensis |
| Solanum aethiopicum |
| Solanum lycopersicum |
| Solanum melongena |
| Solanum pennellii |
| Solenostoma sphaerocarpum |
| Sophora flavescens |
| Sorbus aucuparia |
| Sorghum bicolor |
| Sphagnum palustre |
| Spinacia oleracea |
| Spirodela polyrhiza |
| Spondias mombin |
| Spondias tuberosa |
| Stoneobryum bunyaense |
| Stoneobryum mirum |
| Stratiotes aloides |
| Stylosanthes capitata |
| Stylosanthes macrocephala |
| Stylosanthes pilosa |
| Stylosanthes seabrana |
| Styphnolobium japonicum |
| Suaeda glauca |
| Syntrichia filaris |
| Tamarindus indica |
| Taraxacum mongolicum |
| Taxus chinensis |
| Tetraphis pellucida |
| Tetraplodon fuegianus |
| Theobroma cacao |
| Theobroma grandiflorum |
| Tolypanthus maclurei |
| Toona ciliata |
| Toona sinensis |
| Torminalis glaberrima |
| Treubia lacunosa |
| Trifolium aureum |
| Trifolium grandiflorum |
| Trifolium meduseum |
| Trifolium pratense |
| Trigonella foenum-graecum |
| Trilophozia quinquedentata |
| Tripsacum dactyloides |
| Triticum aestivum |
| Triticum timopheevii |
| Ulota crispa |
| Ulota hutchinsiae |
| Vaccinium macrocarpon |
| Vigna angularis |
| Vigna radiata |
| Viscum album |
| Vitex trifolia |
| Vitis vinifera |
| Welwitschia mirabilis |
| Wiesnerella denudata |
| Zea luxurians |
| Zea mays subsp. mays |
| Zea mays subsp. parviglumis |
| Zea perennis |
| Zingiber leptorrhizum |
| Ziziphus jujuba |
| Ziziphus mauritiana |
| Zostera marina |
| Zygodon viridissimus |
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