convert_ottids_names_tre.py failed to render into a valid newick format?

[Cactusolo]

Hi,

I'm quite sure that this script doesn't work properly. The resultant tree gives error every time when opening it

with newickutils : ERROR: missing ')' at line 0 near '('.

with figtree : Erroe reading tree file: Missing closing ")" in the tree

However, wired enough that:

1. pxcltr doesn't work with resultant tree (/apps/phyx/0.99/launch_phyx: line 12: 15013 Segmentation fault singularity exec ${HPC_SINGULARITY_IMG}/phyx/0.99-xenial.img "$@")
2. while Dendroscope accept it ;)

I think we still need a normal newick formmat.

Miao

Here is the cmd and tree (sorry for the long file) python ./opentree_pytoys/src/convert_ottids_names_tre.py Changbai_ottid.tre Changbai_ottree_node_tip_ottids >test.tre

Changbai_ottid.tre: 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Changbai_ottree_node_tip_ottids: 10210 Tracheophyta 1007992 Euphyllophyta 10218 Spermatophyta 99252 Magnoliophyta 5298374 Mesangiospermae 431495 eudicotyledons 853757 Gunneridae 5316182 Pentapetalae 431493 Oxalidales 372826 Oxalidaceae 372830 Oxalis 323425 Oxalis acetosella 323420 Oxalis acetosella subsp. japonica 429482 Malpighiales 914245 Euphorbiaceae 719243 Euphorbioideae 520955 Euphorbieae 864036 Euphorbia 1076556 Euphorbia humifusa 5147160 Euphorbia sect. Esula 253558 Euphorbia sieboldiana 864028 Euphorbia esula 264674 Euphorbia hylonoma 591092 Euphorbia lucorum 1094341 Acalypheae 560972 Acalypha 607870 Acalypha australis 1000257 Linaceae 393350 Linum stelleroides 62390 Phyllanthaceae 176067 Bridelieae 5763486 Securineginae 365947 Securinega 571181 Securinega suffruticosa 873015 Hypericaceae 1001315 Hypericeae 974217 Hypericum 215651 Hypericum ascyron 304188 Hypericum ascyron var. longistylum 304184 Hypericum attenuatum 952753 Hypericum fauriei 530183 Salicaceae 509390 Saliceae 530178 Populus 148793 Populus koreana 164196 Populus maximowiczii 620851 Populus ussuriensis 819942 Populus davidiana 980993 Populus simonii 458856 Salix (genus in kingdom Archaeplastida) 112994 Salix subfragilis 148767 Salix rosmarinifolia 171988 Salix nummularia 202569 Salix siuzevii 232339 Salix rorida 265785 Salix kangensis 309527 Salix taraikensis 458851 Salix viminalis 459841 Salix arbutifolia 474367 Salix gracilistyla 531931 Salix raddeana 694851 Salix myrtilloides 725919 Salix polyadenia 738770 Salix integra 738780 Salix pentandra 895184 Salix triandra 895186 Salix schwerinii 895197 Salix purpurea 3915133 Chosenia maximowiczii 334625 Salix rotundifolia 5763556 Salix starkeana 5763585 Salix xerophila 95448 Salix matsudana 6105298 Salix yanbianica 224730 Violaceae 295597 Viola (genus in kingdom Archaeplastida) 108248 Viola mandshurica 131176 Viola sacchalinensis 131196 Viola verecunda 382884 Viola selkirkii 870070 Viola yezoensis 436216 Viola biflora 478043 Viola dissecta 643801 Viola dactyloides 746275 Viola epipsila 705822 Viola websteri 741833 Viola mirabilis 753841 Viola collina 959069 Viola rossii 959071 Viola diamantiaca 959080 Viola phalacrocarpa 959086 Viola patrinii 1009601 Viola acuminata 3915383 Viola muehldorfii 478041 Viola variegata 841511 Celastrales 601168 Celastraceae 1035579 Parnassia 1039565 Parnassia palustris 601155 Euonymus 70536 Euonymus verrucosus 601141 Euonymus alatus 1062527 Euonymus maackii 56759 Celastrus 56757 Celastrus orbiculatus 709260 Celastrus flagellaris 483026 Tripterygium 300831 Tripterygium wilfordii 208031 Rosales 658494 Urticaceae 594987 Boehmeria 333302 Boehmeria tricuspis 267703 Urtica (genus in kingdom Archaeplastida) 4729822 Urtica laetevirens 5264237 Urtica angustifolia 1091013 Pilea 691474 Pilea japonica 1091023 Pilea pumila 348789 Laportea 4729826 Laportea bulbifera 630640 Parietaria (genus in kingdom Archaeplastida) 5264256 Parietaria micrantha 672404 Girardinia 736192 Girardinia diversifolia 83996 Cannabaceae 84015 Humulus 74299 Humulus scandens 1014672 Ulmaceae 94969 Ulmus (genus in kingdom Archaeplastida) 572885 Ulmus macrocarpa 1011369 Ulmus laciniata 1011372 Ulmus pumila 4729838 Ulmus davidiana 5763065 Ulmus davidiana var. japonica 582841 Hemiptelea 582829 Hemiptelea davidii 329916 Rhamnaceae 784654 Rhamneae 329914 Rhamnus 228771 Rhamnus davurica 5264448 Rhamnus parvifolia 5763213 Rhamnus koraiensis 5763214 Rhamnus ussuriensis 6109462 Rhamnus diamantiaca 208036 Rosaceae 731147 Rosoideae 891493 Sanguisorbeae 116305 Sanguisorbinae 902629 Sanguisorba 109151 Sanguisorba sitchensis 872135 Sanguisorba tenuifolia 872142 Sanguisorba obtusa 902644 Sanguisorba parviflora 964939 Sanguisorba officinalis 842795 Agrimoniinae 435258 Agrimonia 383278 Agrimonia pilosa 573571 Agrimonia coreana 891491 Potentilleae 827034 Potentilleae unplaced 187939 Potentilla 396153 Potentilla supina 70273 Potentilla supina subsp. paradoxa 307088 Potentilla parvifolia 336103 Potentilla freyniana 475287 Potentilla discolor 538520 Potentilla centigrana 809911 Potentilla longifolia 880112 Potentilla tanacetifolia 902641 Potentilla fragarioides 3904890 Potentilla cryptotaeniae 493031 Potentilla chinensis 493033 Potentilla multifida 713702 Duchesnea 677350 Duchesnea chrysantha 827033 Fragariinae 922848 Dasiphora 782136 Dasiphora fruticosa 559839 Comarum 902637 Comarum palustre 176704 Sibbaldia 176706 Sibbaldia procumbens 208027 Fragaria 1004806 Fragaria orientalis 259066 Rosa 868179 Rosa acicularis 756352 Rosa koreana 868183 Rosa maximowicziana 366725 Colurieae 259063 Geum 77545 Geum aleppicum 972648 Rubus 149341 Rubus pungens 148062 Rubus crataegifolius 412766 Rubus sachalinensis 993560 Rubus arcticus 902631 Rubus chamaemorus 503376 Filipendula 3905512 Filipendula palmata 3905516 Filipendula angustiloba 3905517 Filipendula glaberrima 3905520 Filipendula intermedia 731134 Maloideae 901808 Maleae 489718 Sorbus 317916 Sorbus pohuashanensis 366123 Sorbus alnifolia 208026 Malus 371175 Malus baccata 3902998 Malus komarovii 896383 Malus mandshurica 259068 Pyrus 116277 Pyrus ussuriensis 842028 Crataegus 798280 Crataegus pinnatifida 582036 Crataegus dahurica 582049 Crataegus maximowiczii 376844 Spiraeeae 802382 Aruncus 207990 Aruncus dioicus 489730 Spiraea 437899 Spiraea salicifolia 508587 Spiraea media 882957 Spiraea trichocarpa 3902559 Spiraea dahurica 5527754 Spiraea sericea 376840 Sorbarieae 489722 Sorbaria 873712 Sorbaria sorbifolia 901806 Osmaronieae 7764 Exochorda 717971 Exochorda serratifolia 187946 Prinsepia 769163 Prinsepia sinensis 376842 Amygdaleae 731578 Prunus 42872 Prunus maximowiczii 190311 Prunus salicina 870892 Prunus maackii 3902712 Prunus sachalinensis 376838 Neillieae 738641 Physocarpus 424282 Physocarpus amurensis 366727 Dryadoideae 644048 Dryas (genus in kingdom Archaeplastida) 176708 Dryas octopetala 5336417 Dryas octopetala var. asiatica 11011 Cucurbitales 1006267 Cucurbitaceae 651809 Thladiantheae 841354 Thladiantha 841348 Thladiantha dubia 267709 Fagales 791138 Betulaceae 267715 Betula 731671 Betula platyphylla 46585 Betula schmidtii 495502 Betula davurica 495506 Betula costata 567485 Betula fruticosa 667695 Betula ovalifolia 567488 Betula ermanii 791135 Alnus 639105 Alnus japonica 639096 Alnus hirsuta 1071678 Alnus mandshurica 424333 Corylus 214011 Corylus mandshurica 550611 Corylus heterophylla 619397 Carpinus 799877 Carpinus cordata 438186 Juglandaceae 1072884 Juglans 70093 Juglans mandshurica 267713 Fagaceae 791121 Quercus 429749 Quercus dentata 926284 Quercus wutaishanica 956360 Fabales 560323 Fabaceae 39538 Papilionoideae 563853 Hedysareae 809994 Hedysarum 5532078 Hedysarum ussuriense 440907 Astragalus stevenianus 263091 Astragalus membranaceus 396758 Oxytropis 99396 Oxytropis anertii 63935 Astragalus melilotoides 99398 Astragalus uliginosus 935477 Trifolium 116218 Trifolium repens 839027 Trifolium pratense 1066885 Trifolium lupinaster 1039844 Fabeae 935306 Vicia venosa 136993 Vicia amurensis 539541 Vicia cracca 863684 Vicia pseudo-orobus 863679 Vicia unijuga 942342 Vicia ramuliflora 3928921 Vicia ohwiana 238361 Vicia amoena 1036594 Lathyrus 177905 Lathyrus humilis 177910 Lathyrus komarovii 308795 Lathyrus vaniotii 701246 Lathyrus davidii 883434 Lathyrus palustris 883454 Lathyrus quinquenervius 1018594 Lathyrus pratensis 1036603 Lathyrus odoratus 306104 Melilotus 38042 Melilotus albus 38048 Melilotus officinalis 989938 Melilotus officinalis subsp. suaveolens 459704 Glycine 5533150 Soja 459708 Glycine soja 1063930 Amphicarpaea 213839 Amphicarpaea trisperma 1090339 Desmodieae 1044286 Hylodesmum 383458 Hylodesmum podocarpum 766997 Hylodesmum podocarpum subsp. oxyphyllum 653601 Lespedeza 144305 Lespedeza bicolor 599853 Lespedeza juncea 1044754 Lespedeza davurica 1077029 Lespedeza cyrtobotrya 653608 Kummerowia (genus in kingdom Archaeplastida) 337222 Kummerowia striata 653610 Kummerowia stipulacea 434092 Campylotropis 394356 Campylotropis macrocarpa 49912 Maackia (genus in kingdom Archaeplastida) 49914 Maackia amurensis 711191 Sophora flavescens 404633 Senna 55890 Senna nomame 299382 Polygalaceae 179376 Polygala tatarinowii 378129 Polygala tenuifolia 853283 Polygala sibirica 8844 Brassicales 309271 Brassicaceae 5232954 Turritideae 836246 Turritis 407496 Turritis glabra 546593 Catolobus 682496 Catolobus pendulus 76683 Erysimeae 1037337 Erysimum 36287 Erysimum cheiranthoides 338446 Lepidieae 637146 Lepidium 226076 Lepidium apetalum 806482 Lepidium densiflorum 560483 Cardamineae 609002 Cardamine 33822 Cardamine changbaiana 131963 Cardamine leucantha 609020 Cardamine pratensis 281002 Cardamine yezoensis 338264 Cardamine trifida 740940 Cardamine parviflora 478843 Cardamine impatiens 706548 Cardamine prorepens 192073 Cardamine scutata 3932710 Cardamine komarovii 3932727 Cardamine lyrata 35918 Barbarea 264958 Barbarea orthoceras 341720 Rorippa 720866 Rorippa globosa 509322 Hesperideae 281543 Hesperis 629475 Hesperis sibirica 918850 Draba nemorosa 550043 Arabis hirsuta 3931318 Arabis coronata 5762943 Arabis nipponica 229284 Malvales 1015625 Thymelaeaceae 549854 Daphne 1028544 Daphne pseudomezereum 44291 Daphne pseudomezereum var. koreana 279960 Malvaceae 469942 Malvoideae 83402 Hibiscus 120915 Hibiscus trionum 930069 Malva 297245 Malva verticillata 121966 Malva sylvestris 996483 Tilioideae 30483 Tilia 790022 Tilia mandshurica 5762463 Tilia amurensis 648900 Geraniales 948914 Geraniaceae 948948 Geranium 157260 Geranium dahuricum 298271 Geranium krameri 381970 Geranium erianthum 387583 Geranium soboliferum 65776 Geranium koreanum 298228 Geranium koraiense 387600 Geranium sibiricum 956523 Geranium wilfordii 5748363 Geranium platyanthum 197828 Erodium 1083503 Erodium stephanianum 648898 Myrtales 1015483 Onagraceae 5740793 Onagroideae 5747166 Circaeeae 240815 Circaea 843597 Circaea alpina 240817 Circaea cordata 368031 Circaea lutetiana 5747164 Onagreae 277109 Oenothera 12659 Oenothera biennis 5747162 Epilobieae 139464 Epilobium 916993 Epilobium amurense 940374 Epilobium palustre 980120 Epilobium parviflorum 181424 Epilobium ciliatum 6123151 Epilobium fastigiatoramosum 6123204 Epilobium minutiflorum 215746 Chamerion 139466 Chamerion angustifolium 5740795 Ludwigioideae 312147 Ludwigia (genus in kingdom Archaeplastida) 5762553 Ludwigia prostrata 489493 Lythraceae 886850 Lythrum 886851 Lythrum salicaria 1069308 Vitales 329895 Vitaceae 329909 Parthenocissus 417328 Parthenocissus tricuspidata 329893 Vitis 805071 Vitis amurensis 337874 Ampelopsis 769625 Ampelopsis glandulosa 582639 Ampelopsis glandulosa var. brevipedunculata 432991 Paeoniaceae 747767 Paeonia 352877 Paeonia lactiflora 163406 Paeonia obovata 509332 Crassulaceae 276318 Hylotelephium verticillatum 799697 Hylotelephium erythrostictum 276312 Hylotelephium pallescens 308121 Hylotelephium spectabile 185026 Phedimus hybridus 308119 Phedimus aizoon 581648 Rhodiola sachalinensis 408085 Haloragaceae 730266 Myriophyllum verticillatum 271918 Astilbe chinensis 1023063 Astilboides 756727 Astilboides tabularis 182589 Micranthes punctata 5729610 Micranthes laciniata 497126 Chrysosplenium 126852 Chrysosplenium pilosum 126848 Chrysosplenium pilosum var. sphaerospermum 1040352 Chrysosplenium ramosum 1040354 Chrysosplenium sinicum 500586 Chrysosplenium alternifolium 1040358 Chrysosplenium flagelliferum 6044300 Chrysosplenium lectus-cochleae 365321 Mitella nuda 756719 Saxifraga cernua 1062960 Astilbe koreana 488526 Grossulariaceae 560321 Ribes 729464 Ribes triste 734523 Ribes diacanthum 747529 Ribes komarovii 154642 Ribes rubrum 769233 Ribes maximowiczianum 769228 Ribes mandshuricum 6043975 Ribes horridum 6044004 Ribes pallidiflorum 6044010 Ribes procumbens 596112 lamiids 23736 Lamiales 5263556 Core_Lamiales 1041309 Plantaginaceae 705594 Plantagineae 609811 Plantago 217282 Plantago asiatica 1004414 Plantago depressa 376074 Plantago lanceolata 1004418 Plantago hostifolia 705593 Veroniceae 507032 Veronica 5522034 Beccabunga 115123 Veronica serpyllifolia 6073236 Pseudolysimachium 79014 Veronica longifolia 5522032 Veronica subgenus Veronica 513859 Veronica stelleri 484335 Veronicastrum 484334 Veronicastrum sibiricum 6073463 Veronicastrum tubiflorum 182045 Callitricheae 1080799 Callitriche 338217 Callitriche palustris 705598 Hippurideae 192291 Hippuris 880703 Hippuris vulgaris 83793 Euphrasia 140737 Euphrasia pectinata 415296 Euphrasia maximowiczii 721193 Phtheirospermum 981070 Phtheirospermum japonicum 989660 Pedicularis 205540 Pedicularis grandiflora 914299 Pedicularis spicata 980478 Pedicularis verticillata 980479 Pedicularis resupinata 6088185 Pedicularis mandshurica 447802 Orobancheae 6087731 Orobanche caerulescens 738841 Phrymaceae 5334418 Erythranthe 75214 Erythranthe microphylla 1087001 Phryma 1087002 Phryma leptostachya 544714 Lamiaceae 394658 Nepetoideae 498490 Mentheae 907454 Thymus (genus in kingdom Archaeplastida) 1058608 Thymus serpyllum 830074 Mentha canadensis 636209 Meehania urticifolia 414313 Agastache 485528 Agastache rugosa 165559 Dracocephalum argunense 314683 Nepeta 491364 Nepeta stewartiana 304968 Lycopus (genus in kingdom Archaeplastida) 980292 Lycopus lucidus 586212 Lycopus lucidus var. maackianus 619550 Lycopus uniflorus 314693 Prunella (genus in kingdom Archaeplastida) 709050 Prunella asiatica 498488 Ocimeae 634137 Isodon (genus in kingdom Archaeplastida) 364890 Isodon serra 27323 Elsholtzieae 490129 Elsholtzia 1067793 Elsholtzia ciliata 1074933 Lamioideae 1010876 Lamieae 332799 Lamium 94411 Lamium barbatum 1010868 Leonureae 116381 Leonurus macranthus 789065 Leonurus sibiricus 534798 Phlomideae 6081393 Phlomoides koraiensis 6081401 Phlomoides maximowiczii 534796 Stachydeae 298389 Stachys baicalensis 5800796 Stachys chinensis 534790 Pogostemoneae 732636 Pogostemon 5921548 Pogostemon yatabeanus 1074931 Scutellarioideae 544701 Scutellaria (genus in kingdom Archaeplastida) 357390 Scutellaria laeteviolacea 795166 Scutellaria baicalensis 5793096 Scutellaria regeliana 5793097 Scutellaria dependens 6085810 Scutellaria tuminensis 1074930 Teucrioideae 736688 Amethystea 736685 Amethystea caerulea 659713 Lentibulariaceae 512422 Utricularia 604700 Utricularia vulgaris 615291 Linderniaceae 414644 Lindernia 135588 Lindernia crustacea 91446 Pedaliaceae 628377 Trapella 477458 Trapella sinensis 981058 Siphonostegia 981056 Siphonostegia chinensis 708506 Didymocarpoideae 649722 Trichosporeae 5522099 Loxocarpinae 5512693 Dorcoceras 1053976 Dorcoceras hygrometricum 23723 Oleaceae 483275 Syringa 11353 Syringa wolfii 129929 Syringa pubescens 129924 Syringa pubescens subsp. microphylla 129925 Syringa pubescens subsp. patula 671810 Fraxinus 846439 Fraxinus chinensis 663317 Fraxinus chinensis subsp. rhynchophylla 5261925 Boraginales 6062534 Cynoglossoideae 832281 Brachybotrys 832279 Brachybotrys paridiformis 82995 Myosotis 760140 Myosotis laxa 6063020 Rochelieae 6063021 Eritrichiinae 114241 Lappula redowskii 5144510 Lappula myosotis 6061933 Boraginoideae 6062009 Lithospermeae 791528 Lithospermum erythrorhizon 1050255 Solanales 494850 Convolvulaceae 830575 Cuscuteae 1071030 Cuscuta 5506194 Grammica 5921719 Cuscuta sect. Grammica 286530 Cuscuta chinensis 5921711 Cuscuta subgenus Cuscuta 773450 Cuscuta europaea 5506171 Monogynella 1097404 Cuscuta japonica 302647 Ipomoeeae 494853 Ipomoea 1071036 Ipomoea purpurea 473827 Solanaceae 925265 Physalis alkekengi 524062 Gentianales 1014022 Rubiaceae 521012 Rubieae 297658 Galium kamtschaticum 414746 Galium trifidum 541023 Galium verum 952328 Galium triflorum 3872740 Galium davuricum 3872880 Galium linearifolium 3872920 Galium bungei 3873102 Galium paradoxum 527413 Galium spurium 5232793 Galium spurium var. echinospermum 322051 Rubia 385526 Rubia cordifolia 3872636 Rubia chinensis 5784241 Rubia sylvatica 524059 Apocynaceae 673329 Asclepiadoideae 673333 Asclepiadeae 5518226 Tylophorinae 514638 Vincetoxicum 204095 Vincetoxicum acuminatum 854749 Vincetoxicum atratum 5518230 Cynanchinae 592207 Metaplexis 592208 Metaplexis japonica 816899 Gentianaceae 707911 Gentianeae 168233 Gentiana 65134 Gentiana zollingeri 116672 Gentiana jamesii 162248 Gentiana manshurica 332800 Gentiana pseudoaquatica 332811 Gentiana squarrosa 717875 Gentiana scabra 449120 Gentiana algida 485204 Gentiana triflora 1011762 Swertia 797040 Swertia chinensis 6069337 Swertia veratroides 862721 Halenia (genus in kingdom Archaeplastida) 335878 Halenia corniculata 596121 campanulids 1042120 Asterales 46248 Asteraceae 578390 Cichorioideae 578387 Cichorieae 644707 Hyoseridinae 761940 Sonchus 572930 Sonchus brachyotus 472091 Crepidinae 436307 Ixeris 861688 Ixeris chinensis 5795101 Ixeris polycephala 524978 Taraxacum 425562 Taraxacum coreanum 537525 Crepidiastrum 1011858 Crepidiastrum sonchifolium 472093 Scorzonerinae 485929 Scorzonera 443526 Scorzonera austriaca 472096 Hypochaeridinae 914604 Hypochaeris 430228 Hypochaeris ciliata 454640 Nabalus 475293 Nabalus tatarinowii 119073 Hieraciinae 23821 Hieracium 266289 Hieracium virosum 1095913 Hieracium umbellatum 472092 Lactucinae 515705 Lactuca 678386 Lactuca indica 678396 Lactuca sibirica 5536605 Lactuca raddeana 1084160 Asteroideae 757761 Heliantheae alliance 557772 Heliantheae 217669 Xanthium 709045 Xanthium strumarium 578401 Millerieae 300363 Sigesbeckia 922376 Sigesbeckia pubescens 57535 Coreopsideae 759041 Bidens 86785 Bidens cernua 608098 Bidens tripartita 5794538 Bidens parviflora 557774 Eupatorieae 394959 Eupatorium 680373 Eupatorium lindleyanum 1078746 Eupatorium japonicum 556322 Inulinae 587355 Carpesium 20454 Carpesium macrocephalum 587351 Carpesium cernuum 792531 Carpesium triste 864170 Inula 587344 Inula britannica 557768 Senecioneae 349491 Senecioninae 723076 Senecio 754105 Senecio vulgaris 742737 Senecio nemorensis 480260 Jacobaea 47004 Jacobaea argunensis 117029 Jacobaea cannabifolia 117027 Jacobaea cannabifolia var. integrifolia 784012 Tussilagininae 809312 Tephroseris 812359 Tephroseris pierotii 515694 Ligularia 1010107 Ligularia dentata 1083647 Petasites 896532 Petasites frigidus 557765 Anthemideae 701281 Matricariinae 828101 Achillea 195131 Achillea ptarmica 295550 Achillea alpina 666134 Achillea ptarmicoides 127124 Artemisiinae 692375 Chrysanthemum 228065 Chrysanthemum zawadskii 260062 Chrysanthemum oreastrum 465444 Artemisia 33642 Artemisia mongolica 115033 Artemisia gmelinii 119930 Artemisia apiacea 154471 Artemisia sieversiana 246976 Artemisia manshurica 274425 Artemisia lagocephala 723283 Artemisia stolonifera 723285 Artemisia sylvatica 889813 Artemisia scoparia 1034895 Artemisia lavandulifolia 1034915 Artemisia keiskeana 1084166 Astereae 124080 Australasian lineages 409712 Aster 820265 Aster altaicus 608334 Aster indicus 287847 Aster tataricus 387671 Aster incisus 583685 Aster pekinensis 868082 Aster scaber 965682 Aster maackii 129768 Aster ageratoides 264974 Aster alpinus 202600 Callistephus 202596 Callistephus chinensis 445368 North American clade 643717 Erigeron 747367 Erigeron annuus 323007 Erigeron acris 872351 Solidago 541018 Solidago virgaurea 591422 Conyza 1008406 Conyza canadensis 551663 Eurybia (genus in kingdom Archaeplastida) 1078266 Eurybia sibirica 464144 Gnaphalium 569714 Gnaphalium uliginosum 527107 Carduoideae 54957 Echinopsinae 557760 Cardueae 627940 Carduinae 70338 Cirsium 461560 Cirsium pendulum 834316 Cirsium setosum 1083132 Saussurea 12594 Saussurea sinuata 210428 Saussurea pulchella 348575 Saussurea maximowiczii 519497 Saussurea alpina 636952 Saussurea japonica 716972 Saussurea amurensis 1087441 Saussurea umbrosa 5336737 Saussurea manshurica 5794831 Saussurea grandifolia 465432 Arctium 46196 Arctium lappa 597712 Carduus 249618 Carduus crispus 947023 Himalaiella 210424 Himalaiella deltoidea 415803 Cephanonoplos 415796 Cephalonoplos segetum 733916 Hemisteptia 733911 Hemisteptia lyrata 944237 Synurus (genus in kingdom Archaeplastida) 944238 Synurus deltoides 627941 Centaureinae 569928 Serratula (genus in kingdom Archaeplastida) 795404 Serratula coronata 54959 Carlininae 194043 Atractylodes 194037 Atractylodes lancea 557775 Mutisieae 289565 Leibnitzia 289567 Leibnitzia anandria 935663 Adenocaulon 935632 Adenocaulon himalaicum 694622 Menyanthaceae 128308 Nymphoides 128320 Nymphoides peltata 814227 Menyanthes 1069766 Menyanthes trifoliata 1086303 Campanulaceae 94695 Adenophora (genus in kingdom Archaeplastida) 533067 Adenophora remotiflora 94696 Adenophora divaricata 375154 Adenophora polyantha 817781 Adenophora triphylla 796460 Adenophora pereskiifolia 1028669 Adenophora coronopifolia 1078768 Adenophora grandiflora 533064 Asyneuma japonicum 412607 Campanula punctata 412599 Campanula glomerata 1086294 Lobelia 923372 Lobelia sessilifolia 670513 Codonopsis 39962 Codonopsis ussuriensis 1014057 Codonopsis pilosula 141099 Platycodon 141088 Platycodon grandiflorus 372834 Apiales 1091578 Apiineae 372831 Apiaceae 79260 Apioideae 737499 Saposhnikovia 737496 Saposhnikovia divaricata 287549 Peucedanum praeruptorum 428206 Angelica (genus in kingdom Archaeplastida) 86927 Angelica cartilaginomarginata 628503 Angelica anomala 628505 Angelica amurensis 49588 Angelica dahurica 941676 Angelica gigas 56964 Tordylieae 5795230 Tordyliinae 903079 Heracleum 122463 Heracleum moellendorffii 988987 Peucedanum elegans 298526 Careae 626557 Aegopodium 1012750 Aegopodium alpestre 298518 Scandiceae 166290 Scandicinae 105025 Anthriscus 1074874 Anthriscus sylvestris 713247 Sphallerocarpus 713246 Sphallerocarpus gracilis 200257 Osmorhiza 200265 Osmorhiza aristata 166289 Torilidinae 626553 Torilis 251295 Torilis japonica 200263 Ligusticum jeholense 298524 Oenantheae 498471 Cicuta 49609 Cicuta virosa 652844 Sium 652846 Sium suave 251303 Spuriopimpinella 207718 Spuriopimpinella brachycarpa 1085268 Rupiphila 508622 Rupiphila tachiroei 826294 Pleurospermum uralense 686405 Bupleureae 892024 Bupleurum 486734 Bupleurum chinense 49596 Bupleurum scorzonerifolium 213823 Bupleurum komarovianum 49594 Bupleurum longiradiatum 491614 Bupleurum euphorbioides 524079 Araliaceae 480791 Eleutherococcus 631492 Eleutherococcus senticosus 2116 Eleutherococcus sessiliflorus 11192 Kalopanax 488718 Kalopanax septemlobus 524072 Panax 524063 Panax ginseng 426602 Aralia 322272 Aralia elata 210235 Aralia continentalis 520793 Oplopanax 514826 Oplopanax elatus 659705 Dipsacales 69534 Caprifoliaceae 649885 Lonicera 920874 Lonicera chrysantha 660961 Lonicera maackii 980067 Lonicera ruprechtiana 179065 Lonicera nigra 345664 Lonicera maximowiczii 1086606 Lonicera caerulea 589189 Lonicera caerulea var. edulis 3892213 Lonicera praeflorens 6061433 Lonicera subhispida 393341 Valeriana officinalis 245959 Valeriana amurensis 1035979 Patrinia 231856 Patrinia scabiosifolia 518011 Patrinia intermedia 971855 Patrinia villosa 1035977 Patrinia rupestris 965921 Scabiosa 984352 Scabiosa comosa 702435 Zabelia 716019 Zabelia dielsii 30739 Weigela 32944 Weigela praecox 3892230 Weigela floribunda 757494 Adoxaceae 757503 Viburnum 22570 Viburnum burejaeticum 50892 Viburnum koreanum 117453 Viburnum opulus 51731 Viburnum opulus var. sargentii 1042137 Sambucus 357616 Sambucus buergeriana 589181 Sambucus williamsii 953216 Sambucus manshurica 5746340 Sambucus latipinna 757497 Adoxa 1042115 Adoxa moschatellina 648892 Ericales 47346 Primulaceae 655774 Androsace umbellata 550490 Androsace filiformis 10687 Primula sieboldii 993540 Primula farinosa 588639 Primula fistulosa 411957 Lysimachia clethroides 567411 Lysimachia thyrsiflora 680829 Lysimachia davurica 583308 Trientalis 583307 Trientalis europaea 3900204 Lysimachia barystachys 279976 Actinidiaceae 279984 Actinidia 9477 Actinidia polygama 279941 Actinidia kolomikta 686875 Actinidia arguta 66730 Ericaceae 266533 Ericoideae 687688 Rhodoreae 400112 Rhododendron lapponicum 844320 Rhododendron brachycarpum 695232 Rhododendron aureum 226740 Rhododendron dauricum 230077 Rhododendron redowskianum 750202 Rhododendron parvifolium 687700 Empetreae 99440 Empetrum 162780 Empetrum sibiricum 687686 Phyllodoceae 743803 Phyllodoce (genus in kingdom Archaeplastida) 894628 Phyllodoce caerulea 266537 Vaccinioideae 739256 Vaccinieae 820031 Vaccinium 90281 Vaccinium microcarpum 425957 Vaccinium oxycoccos 994130 Vaccinium uliginosum 113550 Gaultherieae 845656 Chamaedaphne 324770 Chamaedaphne calyculata 266552 Pyroloideae 266555 Monotropeae 384083 Monotropastrum 909403 Monotropastrum humile 539572 Monotropa 824795 Monotropa hypopitys 266557 Pyroleae 18684 Pyrola 18686 Pyrola rotundifolia 106231 Pyrola minor 755291 Pyrola renifolia 680178 Chimaphila 235185 Chimaphila japonica 680175 Chimaphila umbellata 680166 Moneses 680168 Moneses uniflora 680187 Orthilia 3900278 Orthilia obtusata 266550 Arbutoideae 622576 Arctous 622571 Arctous rubra 622578 Arctous alpina 6048990 Ramischia 6048991 Ramischia secunda 289350 Balsaminaceae 928414 Impatiens 5920373 Impatiens subgenus Impatiens 5920379 Impatiens sect. Impatiens 730178 Impatiens textorii 6046308 Impatiens furcillata 120960 Hydrangeaceae 943041 Philadelphus 5144125 Philadelphus schrenkii 313785 Deutzia 666760 Deutzia parviflora 266707 Deutzia parviflora var. amurensis 5144122 Deutzia glabrata 737319 Cornaceae 82463 Cornus 869771 Cornus alba 899880 Alangium 414781 Alangium platanifolium 216628 Caryophyllales 317818 Caryophyllaceae 5920014 Sclerantheae 197077 Minuartia 726134 Minuartia arctica 721242 Minuartia rupestris 5494013 Pseudocherleria 6037086 Pseudocherleria laricina 5920016 Sileneae 154053 Silene (genus in kingdom Archaeplastida) 29433 Silene macrostyla 205375 Silene aprica 728693 Silene baccifera 1056623 Silene repens 1069700 Silene firma 4724301 Silene jenisseensis 6037218 Silene capitata 6037402 Silene koreana 159016 Agrostemma 689981 Agrostemma githago 5920005 Caryophylleae 317820 Dianthus 231868 Dianthus chinensis 432192 Dianthus superbus 28652 Gypsophila 5143826 Gypsophila pacifica 5920003 Arenarieae 923720 Moehringia 320848 Moehringia lateriflora 5920000 Alsineae 842191 Cerastium 732786 Cerastium cerastoides 5728334 Cerastium furcatum 6035536 Cerastium baischanense 432723 Stellaria (genus in kingdom Archaeplastida) 83396 Stellaria neglecta 432718 Stellaria media 689100 Stellaria radians 689106 Stellaria longifolia 1020150 Stellaria bungeana 5728499 Stellaria filicaulis 698780 Pseudostellaria 698777 Pseudostellaria heterophylla 1020152 Pseudostellaria davidii 5728472 Pseudostellaria sylvatica 6035668 Pseudostellaria japonica 689113 Myosoton 689095 Myosoton aquaticum 5920012 Sagineae 459770 Sagina 161892 Sagina japonica 694861 Sagina saginoides 978011 Eremogoneae 291840 Eremogone 5740151 Eremogone juncea 788443 Eremogone capillaris 4724279 Camphorosmoideae 4724280 Camphorosmeae 214363 Bassia (genus in kingdom Archaeplastida) 35500 Bassia scoparia 675983 Bassia prostrata 4724258 Chenopodioideae 4724269 Dysphanieae 70222 Teloxys 70221 Teloxys aristata 892400 Chenopodium 892395 Chenopodium album 202588 Chenopodium acuminatum 6037890 Chenopodium bryoniaefolium 4724265 Oxybasis 827221 Oxybasis glauca 4724260 Chenopodiastrum 499425 Chenopodiastrum hybridum 317808 Amaranthus 892638 Amaranthus retroflexus 33109 Cactineae 63150 Portulacaceae 63152 Portulaca 883494 Portulaca oleracea 904376 Polygonaceae 839947 Polygonoideae 839952 Polygoneae 43733 Polygonum 143996 Polygonum aviculare 5746684 Polygonum ajanense 5920107 Polygonum ochotense 362491 Fallopia (genus in kingdom Archaeplastida) 361565 Fallopia multiflora 362471 Fallopia multiflora var. ciliinervis 362478 Fallopia convolvulus 839950 Rumiceae 904386 Rumex 134757 Rumex acetosa 503466 Rumex maritimus 516846 Rumex crispus 3943857 Rumex aquaticus 3943866 Rumex longifolius 3943892 Rumex gmelinii 6040058 Rumex amurensis 666565 Oxyria 514120 Oxyria digyna 839954 Persicarieae 64965 Persicaria 19860 Persicaria orientalis 19864 Persicaria longiseta 64960 Persicaria senticosa 91320 Persicaria perfoliata 113359 Persicaria thunbergii 143983 Persicaria sagittata 146127 Persicaria amphibia 201229 Persicaria viscosa 302163 Persicaria nepalensis 439770 Persicaria maculosa 478811 Persicaria hydropiperoides 775329 Persicaria pubescens 775333 Persicaria nodosa 1006197 Persicaria lapathifolia 896894 Persicaria hydropiper 927769 Persicaria maackiana 1034576 Persicaria sieboldii 1093317 Persicaria mitis 885332 Bistorta 91303 Bistorta vivipara 5746629 Bistorta manshuriensis 6039778 Bistorta elliptica 885322 Koenigia 951115 Koenigia sect. Aconogonon 6039807 Aconogonon limosum 6039814 Aconogonon platyphyllum 14966 Droseraceae 14968 Drosera 845045 Drosera rotundifolia 5740848 Amyridoideae 945891 Dictamnus 651514 Dictamnus dasycarpus 1016455 Phellodendron 1016461 Phellodendron amurense 873718 Santalaceae 298609 Visceae 914230 Viscum 34127 Viscum coloratum 531039 Aceraceae 948922 Acer 403777 Acer tataricum 403798 Acer tataricum subsp. ginnala 190371 Acer barbinerve 814697 Acer pseudosieboldianum 403786 Acer tegmentosum 456199 Acer triflorum 636265 Acer mandshuricum 1050908 Acer truncatum 872975 Ranunculales 387826 Ranunculaceae 5494506 Delphinieae 756111 Aconitum 377294 Aconitum coreanum 384364 Aconitum monanthum 565431 Aconitum alboviolaceum 625491 Aconitum umbrosum 549540 Aconitum volubile 723180 Aconitum volubile var. latisectum 1064661 Aconitum villosum 5737821 Aconitum kirinense 5737824 Aconitum paniculigerum 549539 Aconitum jaluense 6131382 Aconitum dunhuaense 6131390 Aconitum fusungense 518366 Delphinium 259366 Delphinium maackianum 5494510 Adonideae 1011767 Trollius 230029 Trollius macropetalus 752150 Trollius japonicus 841872 Trollius ledebouri 693553 Adonis 243850 Adonis amurensis 5494507 Ranunculeae 387812 Ranunculus 662449 Ranunculus gmelinii 140131 Ranunculus japonicus 162150 Ranunculus chinensis 162159 Ranunculus ficariifolius 310805 Ranunculus repens 645620 Ranunculus pedatifidus 5737628 Ranunculus franchetii 6133084 Ranunculus tachiroei 5494515 Anemoneae 964052 Clematis 21289 Clematis terniflora 446556 Clematis terniflora var. mandshurica 416093 Clematis brevicaudata 594161 Clematis nobilis 594168 Clematis serratifolia 647742 Clematis heracleifolia 661417 Clematis intricata 661436 Clematis macropetala 3945134 Clematis koreana 282621 Clematis fusca 385038 Anemone 889147 Anemone raddeana 897740 Anemone stolonifera 897748 Anemone amurensis 897752 Anemone reflexa 977458 Anemone sylvestris 5737675 Anemone umbrosa 5737678 Anemone rossii 5737679 Anemone baicalensis 5737693 Anemone dichotoma 5737694 Anemone cathayensis 421851 Pulsatilla 542352 Pulsatilla cernua 5494511 Cimicifugeae 693562 Actaea (genus in kingdom Archaeplastida) 462227 Actaea dahurica 462241 Actaea asiatica 462245 Actaea rubra 512693 Actaea simplex 756501 Eranthis 604763 Eranthis stellata 5494514 Caltheae 279703 Caltha 387810 Caltha palustris 449889 Caltha palustris var. membranacea 5745137 Caltha palustris var. sibirica 5479017 Thalictroideae 947697 Enemion 22673 Enemion raddeanum 948059 Isopyrum 949659 Isopyrum manshuricum 190621 Thalictrum 83785 Thalictrum filamentosum 98297 Thalictrum ichangense 243507 Thalictrum simplex 491705 Thalictrum minus 300814 Thalictrum minus var. hypoleucum 815364 Thalictrum aquilegiifolium 985693 Thalictrum aquilegiifolium var. sibiricum 977693 Thalictrum petaloideum 273547 Thalictrum sparsiflorum 338809 Thalictrum tuberiferum 964055 Aquilegia 203768 Aquilegia viridiflora 4724129 Aquilegia japonica 297866 Berberidaceae 1096858 Epimedium 1096860 Epimedium koreanum 5321950 Plagiorhegma 22675 Plagiorhegma dubium 880484 Berberis 803512 Berberis amurensis 190642 Caulophyllum 229365 Caulophyllum robustum 137435 Gymnospermium 987587 Gymnospermium microrrhynchum 964065 Menispermaceae 855362 Menispermum 855369 Menispermum dauricum 438092 Papaveraceae 5478993 Papaveroideae 1030299 Hylomecon 1030293 Hylomecon japonica 957281 Chelidonium (genus in kingdom Archaeplastida) 957283 Chelidonium majus 438104 Fumarioideae 438103 Corydalis 326188 Corydalis ambigua 818452 Corydalis ochotensis 818458 Corydalis pallida 5727965 Corydalis turtschaninovii 5727987 Corydalis speciosa 5728014 Corydalis repens 6130311 Corydalis buschii 6130640 Corydalis watanabei 402694 Adlumia 5728023 Adlumia asiatica 228826 Ceratophyllales 259039 Ceratophyllaceae 10945 Ceratophyllum (genus in kingdom Archaeplastida) 10930 Ceratophyllum demersum (species in kingdom Archaeplastida) 1058517 Liliopsida 5308424 Petrosaviidae 402582 Commelinales 877745 Commelinaceae 865574 Commelina 877757 Commelina communis 3945840 Streptolirion 3945841 Streptolirion volubile 399488 Pontederiaceae 201049 Monochoria 775189 Monochoria korsakowii 921871 Poales 508090 Poaceae 641464 Pooideae 693952 Meliceae 1019667 Glyceria 348701 Glyceria triflora 348703 Glyceria spiculosa 348707 Glyceria leptolepis 5759332 Glyceria effusa 629679 Melica 513347 Melica nutans 3951750 Melica grandiflora 400259 Schizachne 180834 Schizachne purpurascens 5783135 Schizachne purpurascens subsp. callosa 5737322 Poodae 415737 Poeae 990220 Calamagrostis 182562 Calamagrostis purpurea 188845 Calamagrostis epigeios 211787 Calamagrostis pseudophragmites 533165 Calamagrostis arundinacea 3951443 Calamagrostis nivicola 765663 Agrostis 252175 Agrostis clavata 326461 Agrostis vinealis 307879 Agrostis stolonifera 883668 Agrostis hyemalis 3951408 Agrostis divaricatissima 523563 Deyeuxia 3951483 Deyeuxia angustifolia 5783114 Anthoxanthinae 514147 Anthoxanthum 35194 Anthoxanthum monticola 188813 Anthoxanthum odoratum 788433 Anthoxanthum nipponicum 260288 Aveninae 548935 Trisetum 468433 Trisetum sibiricum 534526 Trisetum spicatum 776539 Phalaridinae 651214 Phalaris 408214 Phalaris arundinacea 5759324 Poeae Chloroplast Group 2 (Poeae type) 5783113 Coleanthinae 591700 Puccinellia 820896 Puccinellia tenuiflora 837414 Poinae 985636 Poa 213082 Poa urssulensis 1079463 Poa pratensis 829772 Poa pratensis subsp. pratensis 814183 Poa nemoralis 923698 Poa palustris 478359 Poa arctica 397788 Poa sibirica 476950 Beckmannia (genus in kingdom Archaeplastida) 35191 Beckmannia syzigachne 811929 Cinna 188848 Cinna latifolia 578771 Phleum 578767 Phleum pratense 1085706 Phleum alpinum 538509 Miliinae 35198 Milium 574589 Milium effusum 538506 Holcinae 710008 Deschampsia 58513 Deschampsia cespitosa 107346 Loliinae 202297 Festuca rubra 413007 Festuca vivipara 607063 Festuca extremiorientalis 3950101 Festuca subalpina 3950246 Festuca jacutica 6022358 Festuca supina 5737321 Triticodae 693954 Triticeae 605366 Elymus 84543 Elymus pendulinus 107998 Elymus excelsus 225994 Elymus sibiricus 717042 Elymus nakaii 606189 Elymus ciliaris 415709 Stipeae 521693 Stipa 244439 Stipa sibirica 493875 Achnatherum 343545 Achnatherum pubicalyx 480490 Achnatherum pekinense 700284 Ptilagrostis 267453 Ptilagrostis malyschevii 693955 Bromeae 83458 Bromus 89410 Bromus pumpellianus 5737323 Brylkinieae 180839 Brylkinia 29439 Brylkinia caudata 119852 PACMAD clade 641461 Panicoideae 5737325 Panicodae 475211 Paniceae 5759510 Cenchrinae 553003 Setaria (genus in kingdom Archaeplastida) 552997 Setaria viridis 604449 Setaria pumila 5759516 Boivinellinae 911853 Echinochloa 578578 Echinochloa oryzoides 5759512 Anthephorinae 990860 Digitaria (genus in kingdom Archaeplastida) 443847 Digitaria ciliaris 6023721 Digitaria linearis 5737327 Andropogonodae 475213 Andropogoneae 5759524 Saccharinae 764804 Miscanthus 764796 Miscanthus sinensis 355148 Miscanthus sacchariflorus 100202 Microstegium 100220 Microstegium vimineum 5759521 Arthraxoninae 1095785 Arthraxon 662170 Arthraxon hispidus 119855 Chloridoideae 1001523 Cynodonteae 352571 Muhlenbergiinae 739168 Muhlenbergia 240005 Muhlenbergia japonica 826561 Muhlenbergia huegelii 928157 Eleusininae 990857 Chloris (genus in kingdom Archaeplastida) 457534 Chloris virgata 1001524 Eragrostideae 402224 Eragrostidinae 587232 Eragrostis 527795 Eragrostis cilianensis 245118 Eragrostis pilosa 6023278 Eragrostis poaeoides 657437 Arundinoideae 5737324 Molinieae 651210 Phragmites 712330 Phragmites australis 931271 Juncaceae 545838 Juncus 184505 Juncus wallichianus 898294 Juncus decipiens 523832 Juncus bufonius 523836 Juncus articulatus 1000029 Juncus compressus 3964846 Juncus krameri 3964942 Juncus haenkei 3964959 Juncus maximowiczii 3964983 Juncus papillosus 3964992 Juncus brachyspathus 1000032 Juncus castaneus 790587 Luzula 279112 Luzula wahlenbergii 415275 Luzula pallescens 334525 Luzula multiflora 898298 Luzula capitata 105574 Cyperaceae 423248 Cyperoideae 948813 Cariceae 397268 Carex 2066 Carex neurocarpa 397258 Carex echinata 13994 Carex disperma 193874 Carex stipata 58705 Carex tenuiflora 4163 Carex canescens 2084 Carex laevissima 3591 Carex dispalata 8152 Carex rupestris 3601 Carex drymophila 72498 Carex lyngbyei 111411 Carex capricornis 174055 Carex atrata 236680 Carex ussuriensis 236682 Carex xiphium 236686 Carex uda 304578 Carex humilis 274858 Carex siderosticta 304593 Carex lanceolata 329194 Carex capillacea 354457 Carex eleusinoides 375543 Carex planiculmis 454183 Carex pallescens 525341 Carex peiktusanii 526978 Carex pilosa 576802 Carex media 685450 Carex rhynchophysa 712222 Carex loliacea 729101 Carex erythrobasis 729104 Carex forficula 729199 Carex biwensis 823028 Carex leiorhyncha 847600 Carex vesicaria 862071 Carex maximowiczii 915773 Carex onoei 929916 Carex globularis 3957829 Carex sordida 3957839 Carex humida 3957845 Carex raddei 3957869 Carex siroumensis 3957873 Carex nervata 3957963 Carex pediformis 3958068 Carex appendiculata 3958206 Carex ulobasis 3958229 Carex remotiuscula 3958261 Carex gmelinii 3958501 Carex lithophila 3958539 Carex glossostigma 3958767 Carex tarumensis 3958905 Carex tuminensis 3959025 Carex kirinensis 3959082 Carex meyeriana 3959114 Carex quadriflora 5744553 Carex longerostrata 6020007 Carex orthostachys 267274 Kobresia 980217 Kobresia myosuroides 423245 Cypereae 627033 Cyperus 236676 Cyperus amuricus 1011062 Cyperus difformis 3959325 Cyperus zollingeri 3959513 Cyperus limosus 1054311 Pycreus 3960043 Pycreus setiformis 423246 Fuireneae 91653 Schoenoplectus 265373 Schoenoplectus tabernaemontani 330788 Schoenoplectiella 306799 Schoenoplectiella komarovii 687329 Bolboschoenus 110695 Bolboschoenus planiculmis 423247 Eleocharideae 790600 Eleocharis 449226 Eleocharis mamillata 6020509 Eleocharis intersita 423249 Scirpeae 267284 Scirpus 110691 Scirpus orientalis 110697 Scirpus karuizawensis 262872 Scirpus radicans 3959165 Scirpus maximowiczii 790595 Eriophorum 172456 Eriophorum gracile 444743 Eriophorum latifolium 738895 Eriophorum vaginatum 913639 Eriophorum russeolum 580889 Eriophorum angustifolium 612686 Trichophorum 262878 Trichophorum alpinum 225264 Typhaceae 613197 Typha 17923 Typha angustifolia 613200 Typha latifolia 928468 Sparganium 120800 Sparganium angustifolium 452423 Sparganium stoloniferum 759031 Sparganium glomeratum 3957200 Sparganium subglobosum 6024527 Sparganium minimum 202244 Rohrbachia 293477 Rohrbachia minima 557124 Asparagales 568878 Orchidaceae 22154 Epidendreae 5919167 Calypsoinae 300570 Corallorhiza 826234 Corallorhiza trifida 214453 Oreorchis 214455 Oreorchis patens 1091749 Calypso (genus in kingdom Archaeplastida) 915007 Calypso bulbosa 852745 Orchidoideae 902467 Cranichideae 73431 Spiranthinae 767488 Spiranthes 761190 Spiranthes sinensis 73438 Goodyerinae 762993 Goodyera 584507 Goodyera repens 976665 Orchideae 73433 Orchidinae 193308 Habenaria 3972481 Habenaria linearifolia 621565 Gymnadenia 621560 Gymnadenia conopsea 1045045 Platanthera 3971835 Platanthera densa 48773 Dactylorhiza 904688 Dactylorhiza viridis 878909 Ponerorchis 345401 Ponerorchis cucullata 852741 Neottieae 875532 Neottia 3987792 Neottia acuminata 3987839 Neottia papilligera 243186 Epipactis 3987935 Epipactis papillosa 852744 Cypripedioideae 530301 Cypripedium 108908 Cypripedium calceolus 262104 Cypripedium yatabeanum 836701 Cypripedium macranthos 836708 Cypripedium guttatum 595054 Malaxideae 5919203 Malaxidinae 712370 Liparis (genus in kingdom Archaeplastida) 910530 Liparis japonica 179401 Malaxis 166575 Malaxis monophyllos 714631 Vanilloideae 5715914 Pogonieae 702803 Pogonia 702801 Pogonia japonica 258473 Amaryllidaceae 17701 Allioideae 842374 Allieae 781603 Allium 626975 Allium schoenoprasum 109767 Allium splendens 650740 Allium victorialis 942175 Allium senescens 346334 Allium neriniflorum 386093 Allium macrostemon 412483 Allium monanthum 295698 Allium thunbergii 497701 Allium condensatum 782212 Allium bidentatum 933619 Allium ledebourianum 20731 Polygonatum 62279 Polygonatum humile 204624 Polygonatum inflatum 260689 Polygonatum involucratum 616151 Polygonatum odoratum 727996 Polygonatum acuminatifolium 1089427 Convallaria 1088891 Convallaria majalis 815516 Maianthemum 62298 Maianthemum dilatatum 260679 Maianthemum japonicum 417437 Maianthemum dahuricum 539415 Maianthemum trifolium 361628 Asparagoideae 748368 Asparagus 672862 Asparagus schoberioides 47206 Hyacinthaceae 981235 Hyacinthoideae 781832 Hyacintheae 978714 Scilla 24752 Scilla scilloides 461417 Xanthorrhoeaceae 981234 Hemerocallidoideae 883105 Hemerocallis 631121 Hemerocallis dumortieri 689603 Hemerocallis minor 997485 Streptopus 3995537 Streptopus koreanus 1087540 Iridaceae 229529 Iris (genus in kingdom Archaeplastida) 43094 Iris setosa 373086 Iris mandshurica 740491 Iris domestica 3998435 Iris kobayashii 577328 Iris ensata 258488 Liliales 781605 Liliaceae 616132 Gagea 146931 Gagea triflora 388168 Gagea serotina 748393 Lilium 73787 Lilium pensylvanicum 884626 Lilium concolor 105372 Lilium concolor var. partheneion 105375 Lilium concolor var. buschianum 689072 Lilium amabile 819134 Lilium distichum 689046 Lilium cernuum 172933 Fritillaria (genus in kingdom Archaeplastida) 702585 Fritillaria ussuriensis 545823 Erythronium 545825 Erythronium japonicum 512520 Clintonia 494155 Clintonia udensis 24750 Smilax (genus in kingdom Archaeplastida) 1028033 Smilax riparia 272789 Smilax nipponica 302313 Smilax sieboldii 430236 Melanthiaceae 597431 Paris 1011470 Paris verticillata 76108 Trillium 76103 Trillium camschatcense 603943 Veratrum 290488 Veratrum nigrum 112384 Veratrum maackii 696806 Veratrum dahuricum 538762 Dioscoreales 781627 Dioscoreaceae 474722 Dioscorea nipponica 399481 Alismatales 481972 Araceae 1085578 Lemnoideae 1008186 Lemna 431388 Lemna minor 483437 Lemna trisulca 431386 Spirodela 814207 Spirodela polyrhiza 1085573 Calloideae 668687 Calla 668688 Calla palustris 708549 Arisaemateae 1027662 Arisaema 727020 Arisaema amurense 1059807 Arisaema heterophyllum 3998944 Arisaema peninsulae 905246 Pinellia 281031 Pinellia ternata 1085577 Orontioideae 807895 Symplocarpus 277364 Symplocarpus nipponicus 1058522 Alismataceae 852506 Alisma 484565 Alisma plantago-aquatica 487679 Alisma plantago-aquatica subsp. orientale 526631 Alisma gramineum 481959 Sagittaria (genus in kingdom Archaeplastida) 962775 Sagittaria trifolia 731515 Sagittaria natans 84269 Hydrocharitaceae 785528 Najas 637151 Najas graminea 329862 Vallisneria 146836 Vallisneria asiatica 1027657 Butomaceae 1027656 Butomus 1027653 Butomus umbellatus 399477 Potamogetonaceae 1048840 Potamogeton 30681 Potamogeton pusillus 242996 Potamogeton crispus 306508 Potamogeton distinctus 431968 Potamogeton compressus 6012989 Potamogeton mandschuriensis 460579 Juncaginaceae 561076 Triglochin 4001356 Triglochin palustre 208899 Scheuchzeriaceae 208898 Scheuchzeria 814198 Scheuchzeria palustris 449210 Tofieldiaceae 140475 Tofieldia 862628 Tofieldia coccinea 276683 Acorales 162554 Acoraceae 1008191 Acorus 1008193 Acorus calamus 31010 Magnoliidae 1022514 Piperales 37785 Aristolochiaceae 656376 Aristolochia manshuriensis 451326 Aristolochia contorta 496568 Asarum 232656 Asarum heterotropoides 165801 Asarum heterotropoides var. mandshuricum 188881 Asarum sieboldii 5919699 Asarum sieboldii var. seoulense 373127 Austrobaileyales 1022517 Schisandraceae 70551 Schisandra 639706 Schisandra chinensis 927972 Nymphaeales 583541 Nymphaeaceae 583523 Nymphaea 537195 Nymphaea tetragona

[Cactusolo]

Problem solved by updating pytoys from github. Also, "pxrlt" from phyx, can rename tip label for a phylogeny tree, by user provide name file, see manual here.

[Cactusolo]

Hi @blackrim ,

I realize this error is from code in "add_missing_taxa_auto.py" line 72:

print tree.get_newick_repr(True)

should be:

print tree.get_newick_repr(True)+";"

so that it will complete a newick format when writing the output tree.

Miao