2b:null 2c:["$","title",null,{"children":"Plant mitochondrial data 'Tree of Life' | Max Brown | Observable"}] 31:T1a4c,chart = { const root = d3 .hierarchy(data, (d) => d.branchset) .sum((d) => (d.branchset ? 0 : 1)) .sort( (a, b) => a.value - b.value || d3.ascending(a.data.length, b.data.length) ); cluster(root); setRadius(root, (root.data.length = 0), innerRadius / maxLength(root)); setColor(root); const svg = d3 .create("svg") .attr("viewBox", [-outerRadius, -outerRadius, width, width]) .attr("font-family", "sans-serif") .attr("font-size", 9); svg.append("g").call(legend); svg.append("style").text(` .link--active { stroke: #000 !important; stroke-width: 1.5px; } .link-extension--active { stroke-opacity: .6; } .label--active { font-weight: bold; } `); const linkExtension = svg .append("g") .attr("fill", "none") .attr("stroke", "#000") .attr("stroke-opacity", 0.25) .selectAll("path") .data(root.links().filter((d) => !d.target.children)) .join("path") .each(function (d) { d.target.linkExtensionNode = this; }) .attr("stroke-width", "0.5") .attr("d", linkExtensionConstant); const link = svg .append("g") .attr("fill", "none") .attr("stroke", "#000") .selectAll("path") .data(root.links()) .join("path") .each(function (d) { d.target.linkNode = this; }) .attr("d", linkConstant) .attr("stroke-width", "1") .attr("stroke", (d) => d.target.color); svg .append("g") .selectAll("text") .data(root.leaves()) .join("text") .attr("dy", ".31em") .attr( "transform", (d) => `rotate(${d.x - 90}) translate(${innerRadius + 4},0)${ d.x < 180 ? "" : " rotate(180)" }` ) .attr("text-anchor", (d) => (d.x < 180 ? "start" : "end")) .attr("font-style", "italic") .attr("fill", "white") .text((d) => d.data.name.replace(/_/g, " ")) .on("mouseover", mouseovered(true)) .on("mouseout", mouseovered(false)); // 1. Build a list of leaf nodes in order (same as your radial tree layout) const rawGcPoints = root .leaves() .map((d) => { const name = d.data.name?.trim().toLowerCase(); const gc = nodeCountMap.get(name); if (gc == null) { console.warn("No GC for", d.data.name); return null; } return { name: d.data.name, gc, angleDeg: d.x }; }) .filter((d) => d !== null); const gcExtent = d3.extent(gcMap.values()); const gcScale = d3 .scaleLinear() .domain(gcExtent) .range([0, outerRadius - innerRadius]); // bar length only const barGroup = svg.append("g").attr("class", "gc-bars"); barGroup .selectAll("line") .data(root.leaves()) .join("line") .attr("x1", (d) => { const angle = ((d.x - 90) * Math.PI) / 180; return innerRadius * Math.cos(angle); }) .attr("y1", (d) => { const angle = ((d.x - 90) * Math.PI) / 180; return innerRadius * Math.sin(angle); }) .attr("x2", (d) => { const gc = gcMap.get(d.data.name?.trim().toLowerCase()); const barLength = gc != null ? gcScale(gc) : 0; const angle = ((d.x - 90) * Math.PI) / 180; return (innerRadius + barLength) * Math.cos(angle); }) .attr("y2", (d) => { const gc = gcMap.get(d.data.name?.trim().toLowerCase()); const barLength = gc != null ? gcScale(gc) : 0; const angle = ((d.x - 90) * Math.PI) / 180; return (innerRadius + barLength) * Math.sin(angle); }) .attr("stroke", "green") .attr("stroke-width", 4) .attr("stroke-opacity", 0.5); const tooltip = d3 .select("body") .append("div") .style("position", "absolute") .style("pointer-events", "none") .style("background", "white") .style("border", "1px solid #ccc") .style("padding", "5px 8px") .style("font-size", "12px") .style("border-radius", "4px") .style("box-shadow", "0 2px 5px rgba(0,0,0,0.2)") .style("display", "none"); barGroup .selectAll("line") .on("mouseover", function (event, d) { const gc = gcMap.get(d.data.name?.trim().toLowerCase()); d3.select(this).attr("stroke", "black"); tooltip .style("display", "block") .html(`${d.data.name}
GC: ${gc?.toFixed(4) ?? "?"}`); }) .on("mousemove", function (event) { tooltip .style("left", event.pageX + 10 + "px") .style("top", event.pageY - 10 + "px"); }) .on("mouseout", function () { d3.select(this).attr("stroke", "green").attr("stroke-opacity", 0.5); tooltip.style("display", "none"); }); // GC content ticks (e.g. 0.40, 0.42, ..., 0.52) const gcTicks = d3.ticks(0.38, 0.48, 6); // adjust range and number as needed const gcScale2 = d3 .scaleLinear() .domain(gcExtent) .range([innerRadius, outerRadius]); // Draw concentric GC rings const gcScaleGroup = svg .append("g") .attr("stroke", "#ccc") .attr("stroke-dasharray", "2,2") .attr("fill", "none"); gcScaleGroup .selectAll("circle") .data(gcTicks) .join("circle") .attr("r", (d) => gcScale2(d)); // Add labels for each ring gcScaleGroup .selectAll("text") .data(gcTicks) .join("text") .attr("y", (d) => -gcScale2(d)) // place along vertical (12 o'clock) .attr("x", 0) .attr("dy", "-0.3em") .attr("text-anchor", "middle") .attr("font-size", 8) .attr("fill", "#555") .text((d) => d.toFixed(3)); const gcLine = d3 .lineRadial() .angle((d) => ((d.angleDeg - 90) * Math.PI) / 180) .radius((d) => gcScale2(d.gc)); const gcPoints = root .leaves() .map((d) => { const name = d.data.name?.trim().toLowerCase(); return { name, angleDeg: d.x, gc: gcMap.get(name) }; }) .filter((d) => d.gc != null); console.log(gcPoints); svg .append("path") .datum(gcPoints) .attr("fill", "none") .attr("stroke", "red") .attr("stroke-opacity", 0.6) .attr("stroke-width", 2) .attr("d", gcLine); function update(checked) { const t = d3.transition().duration(750); linkExtension .transition(t) .attr("d", checked ? linkExtensionVariable : linkExtensionConstant); link.transition(t).attr("d", checked ? linkVariable : linkConstant); } function mouseovered(active) { return function (event, d) { d3.select(this) .classed("label--active", active) .attr("fill", active ? "black" : "white"); d3.select(d.linkExtensionNode) .classed("link-extension--active", active) .raise(); do d3.select(d.linkNode).classed("link--active", active).raise(); while ((d = d.parent)); }; } return Object.assign(svg.node(), { update }); }32:T1dd3,nameToGroup = ({ Acaena_ovalifolia: Dicots, Acer_campestre: Dicots, Adonis_annua: Dicots, Aesculus_hippocastanum: Dicots, Agrostemma_githago: Dicots, Ailanthus_altissima: Dicots, Ajuga_chamaepitys: Dicots, Alisma_plantago_aquatica: Dicots, Alnus_glutinosa: Dicots, Alnus_incana: Dicots, Ammi_majus: Dicots, Antitrichia_curtipendula: Mosses, Aponogeton_distachyos: Dicots, Aquilegia_vulgaris: Dicots, Arabidopsis_thaliana: Dicots, Arabis_hirsuta: Dicots, Arctium_minus: Dicots, Arenaria_serpyllifolia: Dicots, Astragalus_alpinus: Dicots, Astragalus_glycyphyllos: Dicots, Ballota_nigra: Dicots, Barbarea_vulgaris: Dicots, Berberis_vulgaris: Dicots, Blitum_bonus_henricus: Dicots, Brassica_nigra: Dicots, Bromus_sterilis: Dicots, Bryoerythrophyllum_caledonicum: Mosses, Buxus_sempervirens: Dicots, Calendula_officinalis: Dicots, Calliergon_cordifolium: Mosses, Callitriche_obtusangula: Dicots, Calluna_vulgaris: Dicots, Calystegia_soldanella: Dicots, Cardamine_flexuosa: Dicots, Cardamine_hirsuta: Dicots, Carduus_nutans: Dicots, Carex_acutiformis: Sedges, Carex_arenaria: Sedges, Carex_caryophyllea: Sedges, Carex_depauperata: Sedges, Carex_distans: Sedges, Carex_divulsa: Sedges, Carex_extensa: Sedges, Carex_hirta: Sedges, Carex_laevigata: Sedges, Carex_nigra: Sedges, Carex_pendula: Sedges, Carex_riparia: Sedges, Carex_rostrata: Sedges, Carex_sylvatica: Sedges, Carlina_vulgaris: Dicots, Chamaenerion_angustifolium: Dicots, Chenopodium_album: Dicots, Cirsium_eriophorum: Dicots, Climacium_dendroides: Mosses, Comarum_palustre: Dicots, Convolvulus_arvensis: Dicots, Cornus_suecica: Dicots, Corylus_avellana: Dicots, Crataegus_laevigata: Dicots, Cratoneuron_filicinum: Mosses, Cruciata_laevipes: Dicots, Cyperus_fuscus: Sedges, Digitaria_sanguinalis: Dicots, Draba_incana: Dicots, Draba_verna: Dicots, Dryas_octopetala: Dicots, Eleocharis_quinqueflora: Sedges, Epilobium_hirsutum: Dicots, Eriophorum_vaginatum: Sedges, Erodium_maritimum: Dicots, Erodium_moschatum: Dicots, Euonymus_europaeus: Dicots, Euphorbia_lathyris: Dicots, Euphorbia_maculata: Dicots, Euphorbia_peplus: Dicots, Euphrasia_confusa: Dicots, Fagus_sylvatica: Dicots, Fallopia_convolvulus: Dicots, Filago_lutescens: Dicots, Filipendula_ulmaria: Dicots, Fragaria_moschata: Dicots, Fragaria_vesca: Dicots, Frangula_alnus: Dicots, Galeopsis_tetrahit: Dicots, Galium_aparine: Dicots, Geranium_rotundifolium: Dicots, Geum_rivale: Dicots, Geum_urbanum: Dicots, Gnaphalium_supinum: Dicots, Gnaphalium_uliginosum: Dicots, Hedera_helix: Dicots, Herbertus_hutchinsiae: Mosses, Heterocladium_heteropterum: Mosses, Hibiscus_tridactylites: Dicots, Hibiscus_verdcourtii: Dicots, Humulus_lupulus: Dicots, Hydrocotyle_vulgaris: Dicots, Hyocomium_armoricum: Mosses, Hypericum_androsaemum: Dicots, Hypericum_hirsutum: Dicots, Hypericum_pulchrum: Dicots, Hypnum_cupressiforme: Mosses, Ilex_aquifolium: Dicots, Impatiens_glandulifera: Dicots, Impatiens_parviflora: Dicots, Iris_foetidissima: Dicots, Isopterygiella_pulchella: Mosses, Isothecium_myosuroides: Mosses, Jacobaea_maritima: Dicots, Jacobaea_vulgaris: Dicots, Jasione_montana: Dicots, Juncus_effusus: Dicots, Juncus_squarrosus: Dicots, Laburnum_anagyroides: Dicots, Lamium_amplexicaule: Dicots, Lamium_purpureum: Dicots, Lapsana_communis: Dicots, Lathyrus_aphaca: Dicots, Lathyrus_linifolius: Dicots, Leersia_oryzoides: Dicots, Lemna_minuta: Dicots, Lepidium_didymum: Dicots, Ligustrum_vulgare: Dicots, Linaria_vulgaris: Dicots, Logfia_minima: Dicots, Lunularia_cruciata: Mosses, Luzula_pallescens: Dicots, Luzula_sylvatica: Dicots, Lycopus_europaeus: Dicots, Malus_domestica: Dicots, Malus_sylvestris: Dicots, Malus_x_robusta: Dicots, Malva_neglecta: Dicots, Matricaria_chamomilla: Dicots, Matricaria_discoidea: Dicots, Matthiola_sinuata: Dicots, Medicago_arabica: Dicots, Medicago_lupulina: Dicots, Melampyrum_sylvaticum: Dicots, Melittis_melissophyllum: Dicots, Mercurialis_annua: Dicots, Misopates_orontium: Dicots, Moehringia_trinervia: Dicots, Myrica_gale: Dicots, Myriophyllum_alterniflorum: Dicots, Narthecium_ossifragum: Dicots, Nasturtium_officinale: Dicots, Neckera_pumila: Mosses, Ononis_reclinata: Dicots, Orthothecium_rufescens: Mosses, Oxyria_digyna: Dicots, Parietaria_judaica: Dicots, Pentaglottis_sempervirens: Dicots, Persicaria_maculosa: Dicots, Petasites_albus: Dicots, Petasites_hybridus: Dicots, Phragmites_australis: Dicots, Plagiothecium_denticulatum: Mosses, Poa_chaixii: Dicots, Polygonum_aviculare: Dicots, Polygonum_maritimum: Dicots, Polypogon_viridis: Dicots, Polytrichastrum_sexangulare: Mosses, Polytrichum_commune: Mosses, Polytrichum_formosum: Mosses, Populus_nigra: Dicots, Populus_tremula: Dicots, Potamogeton_natans: Dicots, Potentilla_anserina: Dicots, Potentilla_indica: Dicots, Potentilla_sterilis: Dicots, Primula_veris: Dicots, Primula_vulgaris: Dicots, Prunella_vulgaris: Dicots, Prunus_padus: Dicots, Pseudognaphalium_luteoalbum: Dicots, Pseudoscleropodium_purum: Mosses, Pseudotaxiphyllum_elegans: Mosses, Pulicaria_dysenterica: Dicots, Pyrus_communis: Dicots, Quercus_cerris: Dicots, Quercus_ilex: Dicots, Quercus_petraea: Dicots, Quercus_robur: Dicots, Ranunculus_sardous: Dicots, Ranunculus_sceleratus: Dicots, Rhinanthus_minor: Dicots, Rhynchostegiella_tenella: Mosses, Rhynchostegium_megapolitanum: Mosses, Rhytidiadelphus_loreus: Mosses, Ribes_rubrum: Dicots, Ribes_uva_crispa: Dicots, Rosa_agrestis: Dicots, Rosa_canina: Dicots, Rosa_rugosa: Dicots, Rosa_spinosissima: Dicots, Rubus_caesius: Dicots, Rubus_idaeus: Dicots, Salicornia_ramosissima: Dicots, Salix_caprea: Dicots, Salix_cinerea: Dicots, Salix_repens: Dicots, Salix_viminalis: Dicots, Sambucus_nigra: Dicots, Samolus_valerandi: Dicots, Schoenoplectus_lacustris: Sedges, Schoenoplectus_triqueter: Sedges, Scirpus_sylvaticus: Sedges, Scutellaria_galericulata: Dicots, Scutellaria_minor: Dicots, Sherardia_arvensis: Dicots, Solanum_dulcamara: Dicots, Solanum_nigrum: Dicots, Sparganium_emersum: Dicots, Spergula_arvensis: Dicots, Spergularia_bocconei: Dicots, Spergularia_marina: Dicots, Sphagnum_contortum: Mosses, Sphagnum_girgensohnii: Mosses, Sphagnum_tenellum: Mosses, Straminergon_stramineum: Mosses, Syringa_vulgaris: Dicots, Tamarix_gallica: Dicots, Tanacetum_parthenium: Dicots, Tanacetum_vulgare: Dicots, Thalictrum_minus: Dicots, Thuidium_tamariscinum: Mosses, Torilis_japonica: Dicots, Tragopogon_pratensis: Dicots, Trichophorum_cespitosum: Sedges, Trifolium_dubium: Dicots, Trifolium_fragiferum: Dicots, Trifolium_occidentale: Dicots, Trifolium_striatum: Dicots, Trifolium_subterraneum: Dicots, Triglochin_maritima: Dicots, Triglochin_palustris: Dicots, Tripolium_pannonicum: Dicots, Tussilago_farfara: Dicots, Ulmus_glabra: Dicots, Ulota_crispa: Mosses, Umbilicus_rupestris: Dicots, Urtica_dioica: Dicots, Urtica_urens: Dicots, Vaccinium_vitis_idaea: Dicots, Verbascum_nigrum: Dicots, Verbascum_thapsus: Dicots, Verbena_officinalis: Dicots, Veronica_anagallis_aquatica: Dicots, Veronica_arvensis: Dicots, Veronica_scutellata: Dicots, Veronica_serpyllifolia: Dicots, Veronica_triphyllos: Dicots, Veronica_verna: Dicots, Vicia_sativa: Dicots, Viola_odorata: Dicots, Viscum_album: Dicots })33:T797d,polarData = `subgraph_index\tgc\tnode_count\tedge_count\tcoverage\tsegments\ttotal_seq_len\tis_circular\tspecies 0 0.45468518 3 4 666.3333 u27,u28,u29 358496 false Acaena_ovalifolia 0 0.4581512 9 12 1025.3334 u70,u71,u72,u73,u74,u75,u76,u77,u78 750721 false Acer_campestre 0 0.4646034 8 8 147.125 u6,u7,u8,u9,u10,u11,u12,u13 576312 false Adonis_annua 0 0.44918495 9 12 1973.3334 u1,u29,u30,u31,u32,u33,u34,u35,u141 506845 false Aesculus_hippocastanum 0 0.4601219 9 12 2015.6666 u114,u115,u116,u117,u118,u119,u120,u121,u122 244138 false Agrostemma_githago 0 0.4357117 3 4 1660.3334 u39,u40,u41 658069 false Ailanthus_altissima 0 0.4539378 6 8 1162.8334 u25,u26,u27,u28,u29,u30 406560 false Ajuga_chamaepitys 0 0.46069795 11 16 380.0909 u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27 246240 false Alisma_plantago_aquatica 0 0.44930407 3 4 733.3333 u4,u5,u6 506285 true Alnus_glutinosa 1 0.4547208 1 1 704 u11 157103 true Alnus_glutinosa 0 0.44926372 3 4 2040.6666 u2,u3,u18 506361 true Alnus_incana 1 0.43958306 3 4 1134.6666 u24,u25,u26 158118 false Alnus_incana 0 0.45319882 14 19 1578.0714 u100,u101,u102,u103,u104,u105,u106,u107,u108,u109,u110,u111,u112,u113 248792 false Ammi_majus 0 0.41016713 1 1 849 u347 106559 true Antitrichia_curtipendula 0 0.48700464 6 8 258.33334 u28,u29,u30,u31,u32,u33 229972 false Aponogeton_distachyos 0 0.45965007 3 4 1048.3334 u10,u11,u12 408525 false Aquilegia_vulgaris 1 0.4587403 1 1 853 u22 83956 true Aquilegia_vulgaris 0 0.44761297 6 8 1164 u64,u65,u66,u67,u68,u69 363316 false Arabidopsis_thaliana 0 0.44857395 9 12 1346.2222 u28,u29,u30,u31,u32,u33,u34,u35,u36 325981 false Arabis_hirsuta 0 0.49546888 6 8 285.66666 u4,u5,u6,u7,u8,u9 438803 false Arctium_minus 1 0.4521372 9 12 338 u15,u16,u17,u18,u19,u20,u21,u22,u23 284644 false Arctium_minus 0 0.4142371 6 8 5076.5 u59,u60,u61,u62,u63,u64 112059 true Arenaria_serpyllifolia 1 0.43675256 1 1 4951 u8435 39970 true Arenaria_serpyllifolia 2 0.41891384 1 1 3519 u8447 29333 true Arenaria_serpyllifolia 3 0.43276328 1 1 4224 u8523 32103 true Arenaria_serpyllifolia 4 0.4306794 1 1 4282 u8527 34766 true Arenaria_serpyllifolia 5 0.433492 1 1 4078 u8532 32139 true Arenaria_serpyllifolia 6 0.4254655 1 1 5564 u8533 54136 true Arenaria_serpyllifolia 7 0.43486744 1 1 5146 u8537 45108 true Arenaria_serpyllifolia 8 0.4418157 1 1 3756 u8539 33772 true Arenaria_serpyllifolia 9 0.4324535 1 1 3542 u8542 32052 true Arenaria_serpyllifolia 0 0.44935578 5 8 503.4 u56,u57,u58,u59,u60 311629 false Astragalus_alpinus 0 0.45060793 3 4 754.3333 u38,u39,u40 187166 false Astragalus_glycyphyllos 1 0.45254308 1 1 709 u46 173157 true Astragalus_glycyphyllos 0 0.45218349 1 1 1150 u5 148913 true Ballota_nigra 1 0.44808212 1 1 1031 u6 126729 true Ballota_nigra 2 0.44671214 1 1 1111 u7 122298 true Ballota_nigra 0 0.4419005 62 81 2430.6775 u5,u6,u7,u8,u9,u10,u11,u146,u147,u148,u149,u150,u151,u152,u153,u154,u155,u156,u157,u158,u159,u160,u161,u162,u163,u164,u165,u166,u167,u168,u169,u170,u171,u172,u173,u174,u175,u176,u178,u179,u180,u181,u182,u183,u184,u185,u186,u187,u188,u190,u1407,u1409,u1410,u1411,u1412,u1413,u1414,u1415,u1416,u1417,u1418,u1419 428430 false Barbarea_vulgaris 0 0.46078354 9 12 1325.1111 u68,u69,u70,u71,u72,u73,u74,u75,u76 759191 false Berberis_vulgaris 0 0.44618618 9 12 6300.6665 u31,u32,u33,u34,u35,u36,u37,u38,u39 302965 false Blitum_bonus_henricus 0 0.45466194 3 4 404 u40,u41,u42 227052 false Brassica_nigra 0 0.45006895 17 23 941.2353 u36,u37,u38,u39,u40,u41,u42,u43,u44,u45,u46,u47,u48,u49,u50,u51,u96 487981 false Bromus_sterilis 0 0.39578697 1 1 874 u117 106954 true Bryoerythrophyllum_caledonicum 0 0.45108873 17 24 1314.5883 u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27 712289 true Buxus_sempervirens 1 0.44891515 1 1 1022 u32 27239 true Buxus_sempervirens 2 0.45588645 1 1 1073 u33 46709 true Buxus_sempervirens 3 0.4557527 1 1 1001 u34 26657 true Buxus_sempervirens 4 0.4408066 1 1 962 u35 18051 true Buxus_sempervirens 5 0.45504457 1 1 1260 u36 89611 true Buxus_sempervirens 6 0.45842218 1 1 1093 u37 27671 true Buxus_sempervirens 0 0.44203237 6 8 4084.6667 u2,u49,u50,u51,u52,u53 187313 false Calendula_officinalis 1 0.45113444 1 1 3290 u4 128434 true Calendula_officinalis 0 0.40904444 1 1 5104 u10 104705 true Calliergon_cordifolium 0 0.42666012 15 20 1432.2 u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26 318250 false Callitriche_obtusangula 1 0.4278322 1 1 1175 u48 39422 true Callitriche_obtusangula 2 0.42214823 1 1 1039 u49 27334 true Callitriche_obtusangula 0 0.4495003 3 4 2058.6667 u150,u151,u152 431208 false Calluna_vulgaris 0 0.43951336 42 57 3482.8096 u0,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27,u28,u29,u30,u31,u32,u33,u34,u164,u165,u166,u167,u168,u169,u170,u171,u172,u173,u174 297885 false Calystegia_soldanella 0 0.44752067 8 11 1731.875 u37,u38,u39,u40,u41,u2440,u2441,u2442 292844 false Cardamine_flexuosa 0 0.44819677 6 8 1172.3334 u22,u23,u24,u25,u26,u61 290587 false Cardamine_hirsuta 0 0.4491267 6 8 2697 u143,u144,u145,u146,u147,u148 322691 false Carduus_nutans 0 0.40926155 18 24 227.5 u20,u21,u22,u23,u24,u25,u26,u27,u28,u29,u30,u31,u32,u33,u34,u35,u36,u37 1010540 true Carex_acutiformis 1 0.4124185 1 1 187 u54 340186 true Carex_acutiformis 0 0.4146523 13 19 522.2308 u93,u94,u95,u96,u97,u98,u99,u100,u101,u102,u103,u104,u105 1397042 false Carex_arenaria 0 0.41375732 17 23 624.17645 u18,u19,u20,u21,u22,u23,u24,u25,u26,u27,u28,u29,u30,u31,u32,u33,u34 1100023 false Carex_caryophyllea 1 0.4122898 1 1 458 u45 180133 true Carex_caryophyllea 0 0.41534215 26 34 281.15384 u2,u3,u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u51,u52 1403425 false Carex_depauperata 1 0.41282403 1 1 185 u44 166921 true Carex_depauperata 2 0.4090978 1 1 172 u45 132164 true Carex_depauperata 0 0.41188964 12 16 400.41666 u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20 2015487 true Carex_distans 1 0.40487534 1 1 317 u48 106618 true Carex_distans 0 0.41947746 6 8 448.5 u19,u20,u21,u22,u23,u24 1038050 true Carex_divulsa 1 0.41232103 1 1 377 u52 335508 true Carex_divulsa 0 0.41616482 18 24 220 u27,u28,u29,u30,u31,u32,u33,u34,u35,u36,u37,u38,u39,u40,u41,u42,u43,u44 1711647 false Carex_extensa 1 0.41052914 1 1 144 u66 171771 true Carex_extensa 0 0.41036788 12 16 3013.0833 u460,u461,u462,u463,u464,u465,u466,u467,u468,u469,u470,u471 1413439 true Carex_hirta 0 0.40886363 6 8 1023.6667 u4,u5,u103,u104,u105,u106 2738350 false Carex_laevigata 0 0.41559854 15 20 669.26666 u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u112 1446556 false Carex_nigra 0 0.4111546 18 24 386.83334 u28,u29,u30,u31,u32,u33,u34,u35,u36,u37,u38,u39,u40,u41,u42,u43,u44,u45 1374274 false Carex_pendula 1 0.4089948 1 1 283 u51 420844 true Carex_pendula 0 0.41427106 17 22 249.88235 u334,u7338,u7339,u7340,u7341,u7342,u7343,u7344,u7345,u7346,u7347,u7348,u7349,u7350,u7351,u7352,u7353 1205403 false Carex_riparia.k1001.s31.c10 0 0.41352656 18 24 772.7778 u79,u80,u81,u82,u83,u84,u85,u86,u87,u88,u89,u90,u91,u92,u93,u94,u95,u96 1516362 true Carex_rostrata 0 0.41506922 9 12 420.22223 u11,u12,u13,u14,u15,u16,u17,u18,u19 1834260 false Carex_sylvatica 0 0.45481247 15 20 442.6 u1,u2,u3,u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u21 308208 false Carlina_vulgaris 0 0.466259 3 4 961 u109,u110,u111 486356 false Chamaenerion_angustifolium 0 0.43529144 6 8 1494.3334 u11,u12,u13,u14,u15,u16 306277 false Chenopodium_album 0 0.44617283 12 16 1723.4166 u77,u78,u79,u80,u81,u82,u83,u84,u85,u86,u87,u88 311775 false Cirsium_eriophorum 0 0.43859026 3 4 681.3333 u39,u40,u41 107465 false Climacium_dendroides 0 0.44053227 14 19 1105.2142 u26,u27,u28,u29,u30,u31,u32,u33,u34,u35,u36,u37,u54,u55 359018 false Comarum_palustre 0 0.415399 25 36 829.6 u214,u215,u216,u217,u218,u219,u220,u221,u222,u223,u224,u225,u226,u227,u228,u229,u230,u348,u349,u350,u351,u352,u353,u354,u355 320870 false Convolvulus_arvensis 0 0.4568185 3 4 6516 u1,u61,u62 379645 false Cornus_suecica 0 0.4454069 3 4 699 u30,u31,u32 628462 true Corylus_avellana 0 0.45563874 15 20 1516.5333 u69,u70,u71,u72,u73,u74,u75,u76,u77,u78,u79,u125,u126,u127,u128 455503 false Crataegus_laevigata 0 0.40856698 1 1 395 u11 103934 true Cratoneuron_filicinum 0 0.43534127 1 1 1165 u40 124987 true Cruciata_laevipes 1 0.4310964 1 1 1122 u41 109138 true Cruciata_laevipes 0 0.43176943 16 22 1938.6875 u71,u72,u73,u74,u75,u76,u77,u78,u79,u80,u81,u82,u83,u414,u415,u416 561063 false Cymbalaria_muralis 0 0.41461417 9 12 4319.222 u9,u253,u254,u255,u256,u257,u258,u259,u260 896795 false Cyperus_fuscus 0 0.43597484 25 34 1187.64 u66,u67,u68,u69,u70,u71,u72,u73,u74,u75,u76,u77,u78,u79,u80,u81,u82,u83,u505,u506,u507,u508,u509,u510,u511 374806 false Digitaria_sanguinalis 0 0.45163536 1 1 2526 u54 284340 true Draba_incana 0 0.4477911 11 16 3088.818 u37,u38,u39,u40,u41,u42,u43,u44,u118,u119,u120 281090 false Draba_verna 0 0.4676877 6 8 2503.5 u0,u1,u7,u8,u143,u144 352388 false Dryas_octopetala 0 0.4186835 14 19 426.14285 u29,u30,u31,u32,u33,u34,u35,u36,u37,u38,u39,u40,u41,u284 1967042 false Eleocharis_quinqueflora 0 0.46146515 3 4 1813.3334 u152,u153,u154 430790 true Epilobium_hirsutum 0 0.4206929 15 20 252.2 u91,u92,u93,u94,u95,u96,u97,u98,u99,u100,u101,u102,u103,u104,u105 1787323 false Eriophorum_vaginatum.k1001.s31.c40 0 0.42293036 9 12 1129.3334 u53,u54,u55,u56,u57,u58,u59,u60,u136 203359 false Erodium_maritimum 1 0.41749483 1 1 874 u73 43167 true Erodium_maritimum 2 0.42027393 1 1 915 u74 57315 true Erodium_maritimum 0 0.4379261 1 1 1955 u132 72752 true Erodium_moschatum 1 0.42355445 1 1 2032 u133 43253 true Erodium_moschatum 2 0.42411736 1 1 2666 u138 55968 true Erodium_moschatum 3 0.42531252 1 1 1714 u148 30159 true Erodium_moschatum 4 0.4359711 1 1 1456 u152 27144 true Erodium_moschatum 5 0.41997662 1 1 1613 u158 29935 true Erodium_moschatum 0 0.45060158 15 20 1574.8667 u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27,u28,u29,u30,u31 1118174 false Euonymus_europaeus 1 0.45076564 1 1 1365 u42 326784 true Euonymus_europaeus 0 0.43991545 15 20 1613.6 u0,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u57,u58 860372 false Euphorbia_lathyris 1 0.4469792 1 1 925 u48 42257 true Euphorbia_lathyris 2 0.43578103 1 1 1089 u49 86353 true Euphorbia_lathyris 3 0.43691838 1 1 901 u50 32775 true Euphorbia_lathyris 0 0.44369712 6 8 730 u17,u18,u19,u20,u21,u22 616868 false Euphorbia_maculata 1 0.43465278 1 1 523 u37 79705 true Euphorbia_maculata 0 0.4347901 11 13 1208.6364 u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u73 624118 true Euphorbia_peplus 1 0.4401388 4 4 1346.25 u36,u37,u38,u89 127280 false Euphorbia_peplus 2 0.4390799 1 1 959 u53 49647 true Euphorbia_peplus 0 0.44879463 9 12 1730 u44,u45,u46,u47,u48,u49,u50,u51,u196 320522 false Euphrasia_confusa 1 0.44467303 1 1 1315 u89 113254 true Euphrasia_confusa 0 0.47617322 5 7 827.2 u35,u36,u37,u75,u76 508244 false Fagus_sylvatica 0 0.4458151 8 12 1587.25 u7,u8,u9,u10,u11,u12,u13,u14 359074 false Fallopia_convolvulus 0 0.4631034 8 11 1848.625 u13,u14,u15,u576,u577,u578,u8767,u8768 234771 false Filago_lutescens 0 0.42719394 11 16 378.0909 u55,u56,u57,u58,u59,u60,u61,u62,u63,u64,u65 868182 false Filipendula_ulmaria 0 0.44891796 3 4 5173.6665 u1210,u1211,u1212 349547 false Fragaria_moschata 0 0.44707114 9 12 2196.3333 u35,u36,u37,u38,u39,u40,u41,u42,u43 343999 false Fragaria_vesca 0 0.45008686 6 8 2164.3333 u26,u27,u28,u29,u30,u31 481712 false Frangula_alnus 0 0.44701305 3 4 477 u18,u19,u20 192857 false Galatella_linosyris 1 0.4477699 1 1 236 u22 61545 true Galatella_linosyris 0 0.45471272 3 4 474.66666 u48,u49,u50 71944 false Galeopsis_tetrahit 1 0.4538831 1 1 451 u58 69725 true Galeopsis_tetrahit 2 0.45445803 1 1 382 u59 39513 true Galeopsis_tetrahit 3 0.4477138 1 1 429 u60 40307 true Galeopsis_tetrahit 4 0.4534153 1 1 398 u61 44886 true Galeopsis_tetrahit 5 0.43490273 1 1 244 u62 16652 true Galeopsis_tetrahit 6 0.46466595 1 1 269 u63 25924 true Galeopsis_tetrahit 7 0.4652339 1 1 258 u64 20566 true Galeopsis_tetrahit 8 0.45883325 1 1 358 u67 27838 true Galeopsis_tetrahit 9 0.42920446 1 1 181 u68 9478 true Galeopsis_tetrahit 0 0.44658446 12 16 2314.4167 u3,u23,u24,u25,u26,u27,u28,u29,u30,u96,u97,u98 217125 false Galium_aparine 0 0.43823013 1 1 778 u38 189097 true Galium_uliginosum 0 0.4207922 9 12 1832.1111 u633,u634,u635,u636,u637,u638,u639,u640,u7810 254805 true Geranium_molle 1 0.40844265 1 1 2636 u7557 68083 true Geranium_molle 2 0.41200632 1 1 2500 u7558 72795 true Geranium_molle 0 0.41416252 3 4 1412 u56,u57,u58 331981 false Geranium_rotundifolium 0 0.43732256 8 11 1620.75 u2,u3,u79,u80,u81,u82,u83,u150 324628 false Geum_rivale 0 0.43731356 8 11 836.25 u1,u2,u16,u17,u18,u19,u20,u33 324628 false Geum_urbanum 0 0.44747013 1 1 1290 u93 84609 true Gnaphalium_supinum 1 0.45232794 1 1 1522 u94 166156 true Gnaphalium_supinum 0 0.45559525 1 1 1158 u25 196229 true Gnaphalium_uliginosum 0 0.4463503 48 67 966.4792 u0,u1,u2,u3,u4,u5,u6,u7,u8,u12,u13,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u28,u29,u30,u31,u32,u33,u34,u35,u36,u37,u38,u39,u40,u41,u42,u43,u44,u45,u46,u146,u147,u148,u149,u150,u151 649797 false Hedera_helix 0 0.44585803 1 1 608 u5 162942 true Herbertus_hutchinsiae 0 0.41032627 1 1 3897 u16 106079 true Heterocladium_heteropterum 0 0.44587436 9 12 1583.6666 u31,u32,u33,u34,u35,u36,u37,u38,u39 519880 false Hibiscus_tridactylites 0 0.45954207 6 8 1441.8334 u23,u24,u25,u26,u27,u103 428275 false Hibiscus_verdcourtii 1 0.45190325 1 1 962 u46 106660 true Hibiscus_verdcourtii 0 0.45733938 1 1 75 u25 401295 true Humulus_lupulus.k1001.s31.c10 0 0.44668835 10 15 1719.2 u48,u49,u50,u51,u52,u53,u54,u55,u56,u137 567568 false Hydrocotyle_vulgaris 0 0.40913922 1 1 2892 u21 104473 true Hyocomium_armoricum 0 0.43420008 1 1 615 u14 75608 true Hypericum_androsaemum 1 0.44140592 1 1 697 u15 103449 true Hypericum_androsaemum 2 0.43980783 1 1 599 u16 99282 true Hypericum_androsaemum 3 0.4425651 1 1 729 u17 140002 true Hypericum_androsaemum 0 0.44816327 3 4 1347 u63,u64,u65 474752 false Hypericum_hirsutum 0 0.42999712 3 4 1085.3334 u52,u53,u54 218728 false Hypericum_pulchrum 1 0.4421689 1 1 882 u64 276564 true Hypericum_pulchrum 0 0.41077238 1 1 456 u6 104805 true Hypnum_cupressiforme 0 0.4556636 1 1 1953 u214 539365 true Ilex_aquifolium 0 0.45122352 3 4 1000.6667 u95,u96,u97 43029 false Impatiens_glandulifera 1 0.45680895 1 1 1055 u103 22933 true Impatiens_glandulifera 2 0.43639153 1 1 1186 u104 37157 true Impatiens_glandulifera 3 0.45414233 1 1 883 u105 32023 true Impatiens_glandulifera 4 0.44273973 1 1 939 u106 27375 true Impatiens_glandulifera 5 0.4573301 1 1 852 u107 27162 true Impatiens_glandulifera 6 0.44545949 1 1 972 u108 29446 true Impatiens_glandulifera 7 0.4367981 1 1 779 u109 25110 true Impatiens_glandulifera 8 0.43952712 1 1 1195 u111 48807 true Impatiens_glandulifera 9 0.42036313 1 1 555 u112 14045 true Impatiens_glandulifera 10 0.4407154 1 1 657 u113 13587 true Impatiens_glandulifera 11 0.42455608 1 1 1185 u114 29565 true Impatiens_glandulifera 12 0.43869764 1 1 925 u115 30529 true Impatiens_glandulifera 13 0.449267 1 1 948 u116 25989 true Impatiens_glandulifera 14 0.4434897 1 1 1168 u118 40267 true Impatiens_glandulifera 15 0.4282222 1 1 744 u126 19226 true Impatiens_glandulifera 0 0.44210774 1 1 688 u333 25392 true Impatiens_parviflora 1 0.44756982 1 1 611 u335 19340 true Impatiens_parviflora 2 0.45236984 1 1 735 u339 32175 true Impatiens_parviflora 3 0.45429504 1 1 1125 u341 25774 true Impatiens_parviflora 4 0.44446072 1 1 910 u344 40953 true Impatiens_parviflora 5 0.4213872 1 1 543 u345 14158 true Impatiens_parviflora 6 0.44898793 1 1 765 u349 26925 true Impatiens_parviflora 7 0.44221762 1 1 834 u350 35227 true Impatiens_parviflora 8 0.44603762 1 1 909 u351 27269 true Impatiens_parviflora 9 0.42840642 1 1 678 u353 20777 true Impatiens_parviflora 10 0.43981642 1 1 955 u358 49457 true Impatiens_parviflora 11 0.4383142 1 1 749 u362 24487 true Impatiens_parviflora 12 0.44054395 1 1 810 u364 31620 true Impatiens_parviflora 13 0.4368042 1 1 935 u365 36648 true Impatiens_parviflora 14 0.44612333 1 1 1004 u372 26208 true Impatiens_parviflora 15 0.46156344 1 1 683 u373 27708 true Impatiens_parviflora 0 0.4714321 6 8 636.1667 u18,u19,u20,u21,u22,u23 418224 false Iris_foetidissima 0 0.41098836 1 1 2348 u3 105093 true Isopterygiella_pulchella 0 0.41133606 1 1 429 u74 105398 true Isothecium_myosuroides 0 0.44953674 8 12 848.875 u128,u129,u130,u131,u132,u133,u134,u135 316088 false Jacobaea_maritima 0 0.45126382 3 4 469.33334 u103,u104,u197 280156 true Jacobaea_vulgaris 0 0.42731604 3 4 1856 u161,u162,u307 322876 false Jasione_montana 0 0.44841146 3 4 1104 u75,u76,u77 488823 false Juncus_effusus 0 0.4439969 8 11 1049.125 u3,u4,u153,u154,u155,u156,u157,u158 563791 false Juncus_squarrosus 1 0.44197965 1 1 1027 u2432 422076 true Juncus_squarrosus 0 0.44789144 3 4 1490.3334 u2,u19,u20 421492 false Laburnum_anagyroides 0 0.44883236 6 8 2507.1667 u23,u24,u25,u26,u27,u28 299451 false Lamium_amplexicaule 0 0.45051125 15 20 1433.4667 u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u61,u62,u63 296376 false Lamium_purpureum 0 0.44438213 8 11 339.75 u41,u42,u43,u44,u45,u46,u47,u48 293943 false Lapsana_communis 0 0.45075354 3 4 594.6667 u8,u9,u10 370128 false Lathyrus_aphaca 0 0.45381647 17 23 512.2941 u3,u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u58 427013 false Lathyrus_linifolius 0 0.43757012 6 8 267.16666 u14,u15,u16,u17,u18,u19 380293 true Leersia_oryzoides 0 0.44841507 1 0 302 u16 186789 false Lemna_minuta 0 0.4495006 1 1 5631 u14 263508 true Lepidium_didymum 0 0.45363364 3 4 1444 u7,u8,u68 965431 true Ligustrum_vulgare 0 0.44989553 3 4 1345.6666 u2,u15,u16 320061 false Linaria_vulgaris 1 0.44690672 1 1 1023 u20 138671 true Linaria_vulgaris 0 0.42327195 40 56 3529.775 u0,u1,u2,u3,u4,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27,u28,u29,u31,u32,u33,u34,u272,u273,u274,u275,u276,u277,u278,u279,u280,u281 519299 false Lobelia_dortmanna 0 0.42805728 16 22 6591.875 u16,u1076,u1077,u1078,u1079,u1080,u1081,u1082,u1083,u1084,u1085,u1086,u1087,u1088,u1089,u5539 511945 false Lobelia_urens 0 0.4550525 1 1 690 u19 221959 true Logfia_minima 0 0.4260659 1 1 2028 u3 191461 true Lunularia_cruciata 0 0.46725544 3 4 232 u22,u23,u24 653022 false Luzula_pallescens 0 0.4551853 12 16 908.25 u46,u47,u48,u49,u50,u51,u52,u53,u54,u55,u56,u57 649416 false Luzula_sylvatica 0 0.45149148 9 12 1309.1111 u40,u41,u42,u43,u87,u88,u89,u90,u91 295850 false Lycopus_europaeus 0 0.4503072 23 32 863.95654 u5,u6,u7,u8,u9,u10,u143,u144,u145,u146,u147,u148,u149,u150,u151,u152,u153,u154,u155,u156,u157,u257,u258 418803 false Malus_domestica 0 0.45786762 3 4 676 u46,u47,u48 392784 false Malus_sylvestris 0 0.45693567 3 4 664.3333 u37,u38,u39 374153 false Malus_x_robusta 0 0.44866502 12 16 1501.8334 u52,u53,u54,u55,u56,u57,u58,u59,u60,u61,u62,u63 382910 false Malva_neglecta 1 0.45348895 1 1 1175 u88 165810 true Malva_neglecta 0 0.45490366 1 1 849 u24 220295 true Matricaria_chamomilla 0 0.45543537 3 4 1705.3334 u2,u3,u17 225232 false Matricaria_discoidea 0 0.44408196 11 15 1602.909 u29,u30,u31,u32,u33,u34,u117,u118,u119,u120,u121 424756 false Matthiola_sinuata 0 0.4432165 17 24 1258.1765 u49,u50,u51,u52,u53,u54,u55,u56,u57,u58,u151,u152,u153,u154,u155,u156,u157 325268 true Medicago_arabica 0 0.45691788 3 4 1697 u180,u181,u182 297329 false Medicago_lupulina 0 0.44422212 23 35 462.73914 u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u57,u58,u59,u60,u61 299490 false Melampyrum_sylvaticum 0 0.45184657 3 4 2336.6667 u57,u58,u59 360663 false Melittis_melissophyllum 0 0.38644722 5 7 709.8 u30,u31,u88,u89,u90 432385 false Mercurialis_annua 0 0.4455613 1 1 681 u12 569953 true Misopates_orontium 0 0.42934048 6 8 3385 u17,u18,u19,u20,u21,u22 334854 false Moehringia_trinervia 0 0.45384598 1 1 600 u24 486469 true Myrica_gale 0 0.450528 12 16 2253.9167 u193,u194,u195,u196,u197,u198,u199,u200,u201,u202,u203,u2270 393920 false Myriophyllum_alterniflorum 0 0.45889223 3 4 2774.6667 u20,u21,u22 307910 false Narthecium_ossifragum 1 0.45902744 1 1 1863 u65 100909 true Narthecium_ossifragum 0 0.4485352 3 4 2480.3333 u59,u60,u61 287210 false Nasturtium_officinale 0 0.41155 1 1 177 u12 104381 true Neckera_pumila 0 0.45287064 1 1 3395 u292 194974 true Ononis_reclinata 1 0.44612923 1 1 2863 u296 125569 true Ononis_reclinata 0 0.38921955 3 4 1577 u53,u6695,u6696 106897 false Orthothecium_rufescens 0 0.4436578 3 4 4032.3333 u10,u358,u359 252509 false Oxyria_digyna 1 0.45553502 3 4 3070 u486,u487,u488 158706 false Oxyria_digyna 0 0.44698715 1 1 1009 u92 113265 true Parietaria_judaica 1 0.4414666 1 1 999 u93 108468 true Parietaria_judaica 2 0.4456714 1 1 1074 u94 215982 true Parietaria_judaica 0 0.44970283 5 8 2101.2 u300,u301,u302,u303,u304 326907 true Pentaglottis_sempervirens 0 0.44303474 12 16 3150.5 u0,u36,u37,u38,u39,u40,u41,u42,u43,u44,u45,u46 391600 false Persicaria_maculosa 0 0.44032562 6 8 649.6667 u22,u23,u24,u25,u26,u76 261812 true Petasites_albus 1 0.45287332 1 1 427 u33 46810 true Petasites_albus 0 0.4464919 2 4 494.5 u2,u43 302891 false Petasites_hybridus 0 0.43600777 12 16 506.33334 u1,u2,u3,u4,u5,u6,u7,u8,u9,u10,u11,u30 476252 false Phragmites_australis 0 0.4122997 1 1 3666 u20 104783 true Plagiothecium_denticulatum 0 0.44984433 12 16 484.5 u35,u36,u37,u38,u39,u40,u41,u42,u43,u44,u45,u46 458472 false Poa_chaixii 0 0.44518483 1 1 1089 u41 334661 true Polygonum_aviculare 0 0.44535673 9 12 4820.8887 u5009,u5010,u5011,u5012,u5013,u5014,u5015,u5016,u8662 353784 false Polygonum_maritimum 0 0.4440303 9 12 711 u0,u13,u14,u15,u16,u17,u18,u19,u20 560672 false Polypogon_viridis 0 0.40562174 1 1 1384 u78 116192 true Polytrichastrum_sexangulare 0 0.40461966 1 1 968 u33 115506 true Polytrichum_commune 0 0.40384465 1 1 1471 u417 116057 true Polytrichum_formosum 0 0.44658193 1 1 1145 u129 281899 true Populus_nigra 1 0.45021793 1 1 1208 u130 336788 true Populus_nigra 2 0.44787022 1 1 1092 u131 186333 true Populus_nigra 0 0.4474422 1 1 1371 u91 783737 true Populus_tremula 0 0.47705984 3 4 544.3333 u90,u91,u92 258143 false Potamogeton_natans 0 0.45137915 3 4 348 u49,u50,u51 290869 false Potentilla_anserina 0 0.44955325 3 4 1948.3334 u15,u16,u17 435184 false Potentilla_indica 0 0.4516963 6 8 979.6667 u22,u23,u24,u25,u26,u27 450425 false Potentilla_sterilis 0 0.47226992 5 8 5108.2 u0,u4,u5,u141,u142 326576 false Primula_veris 0 0.45086107 6 8 5104.8335 u1,u37,u38,u39,u40,u76 327389 false Primula_vulgaris 0 0.44051704 3 4 926.6667 u120,u121,u122 293995 false Prunella_vulgaris 0 0.45438543 3 4 3558 u60,u61,u62 278483 false Prunus_padus 1 0.45761436 1 1 2737 u76 156645 true Prunus_padus 0 0.4564054 3 4 2456 u3,u38,u39 234032 false Pseudognaphalium_luteoalbum 0 0.41021115 1 1 1414 u40 105336 true Pseudoscleropodium_purum 0 0.3804654 3 4 2955.3333 u170,u3349,u3350 107297 false Pseudotaxiphyllum_elegans 0 0.44648814 8 11 704.625 u19,u20,u21,u22,u23,u24,u25,u26 353925 false Pulicaria_dysenterica 0 0.454262 1 1 998 u78 184092 true Pyrus_communis 1 0.4512675 1 1 1051 u79 260391 true Pyrus_communis 0 0.45088413 30 43 989.56665 u0,u1,u2,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u207,u208,u209,u210,u211,u212,u213,u214 1043274 false Quercus_cerris 1 0.45081234 6 8 936.3333 u95,u96,u97,u98,u99,u100 398305 true Quercus_cerris 2 0.43971783 1 1 805 u131 78962 true Quercus_cerris 0 0.45420378 17 24 1681.1177 u62,u63,u64,u65,u66,u67,u68,u69,u70,u71,u72,u73,u74,u75,u76,u228,u229 540667 false Quercus_ilex 0 0.45854422 8 11 3009.875 u21,u22,u23,u24,u25,u26,u27,u28 375478 false Quercus_petraea 0 0.4561322 9 12 855.7778 u48,u49,u50,u51,u52,u53,u54,u55,u56 377745 false Quercus_robur 0 0.46062264 9 12 1033 u21,u22,u23,u24,u25,u26,u27,u28,u29 828996 true Ranunculus_sardous 0 0.45952994 14 19 983.9286 u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18 850209 false Ranunculus_sceleratus 0 0.4550072 8 11 1682.25 u100,u101,u102,u103,u104,u105,u226,u227 94423 false Rhinanthus_minor 1 0.43516532 1 1 2511 u119 75438 true Rhinanthus_minor 2 0.4489938 1 1 2357 u120 44475 true Rhinanthus_minor 3 0.44938353 1 1 2107 u121 39256 true Rhinanthus_minor 4 0.44567773 1 1 2428 u122 62525 true Rhinanthus_minor 5 0.4376931 1 1 1552 u123 27188 true Rhinanthus_minor 0 0.41107067 1 1 327 u14 105269 true Rhynchostegiella_tenella 0 0.4093343 1 1 469 u5 104582 true Rhynchostegium_megapolitanum 0 0.40875074 1 1 708 u63 106094 true Rhytidiadelphus_loreus 0 0.4548293 12 16 2860.3333 u15,u333,u334,u335,u336,u337,u338,u339,u340,u341,u1221,u1222 523661 false Ribes_rubrum 0 0.4585166 3 4 1669 u87,u88,u89 444788 false Ribes_uva_crispa 0 0.45397374 1 1 1047 u112 271910 true Rosa_agrestis 0 0.4518716 3 4 617.3333 u16,u17,u18 260972 false Rosa_canina 0 0.45232162 1 1 827 u23 303366 true Rosa_rugosa 0 0.4630356 3 4 2243 u90,u91,u92 287776 false Rosa_spinosissima 0 0.43943694 6 8 555.1667 u53,u54,u55,u56,u57,u58 406798 false Rubus_caesius 0 0.44236872 3 4 1094.6666 u52,u53,u54 406600 false Rubus_idaeus 0 0.4466888 18 24 3541.2778 u589,u590,u591,u592,u593,u594,u595,u596,u597,u598,u599,u600,u601,u602,u603,u6852,u6853,u6854 321844 false Salicornia_ramosissima 0 0.45179594 3 4 624 u78,u79,u247 475983 false Salix_caprea 1 0.45433578 1 1 737 u102 133113 true Salix_caprea 0 0.44522533 6 8 784.1667 u99,u100,u101,u102,u103,u345 654430 false Salix_cinerea 0 0.4526243 3 4 1186.3334 u38,u39,u40 641629 false Salix_repens 0 0.4497466 3 4 1033.6666 u23,u24,u25 316484 false Salix_viminalis 1 0.4492109 1 1 949 u42 319291 true Salix_viminalis 0 0.4580783 5 8 398.6 u24,u25,u26,u27,u28 718256 false Sambucus_nigra.k1001.s31.c40 0 0.45101547 3 4 2191.6667 u42,u43,u150 432016 false Samolus_valerandi 0 0.45073983 3 4 2432.6667 u63,u64,u65 356609 false Saxifraga_aizoides 1 0.4473405 1 1 2127 u67 77270 true Saxifraga_aizoides 0 0.43165794 21 28 179.5238 u63,u64,u65,u66,u67,u68,u69,u70,u71,u72,u73,u74,u75,u76,u77,u78,u79,u80,u81,u82,u179 2074166 false Schoenoplectus_lacustris.k1001.s31.c40 0 0.42894122 21 28 569.7619 u42,u43,u44,u45,u46,u47,u48,u49,u50,u51,u52,u53,u54,u55,u56,u57,u58,u59,u60,u61,u62 1614964 false Schoenoplectus_triqueter 0 0.41511378 20 27 341.15 u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u21,u22,u23,u24,u25,u26,u27,u28,u29 1961564 false Scirpus_sylvaticus 0 0.45466155 1 1 1175 u276 327327 true Scutellaria_galericulata 0 0.4457419 6 8 2260.6667 u28,u29,u30,u31,u32,u138 376501 false Scutellaria_minor 0 0.45652995 3 4 1352 u8,u9,u10 264779 false Senecio_sylvaticus 0 0.43111765 2 4 1513 u48,u49 192771 false Sherardia_arvensis 0 0.45442575 9 12 1599.7778 u29,u30,u31,u32,u33,u34,u35,u36,u62 397783 false Solanum_dulcamara 1 0.44908735 1 1 1128 u43 56430 true Solanum_dulcamara 0 0.45446074 9 12 1256.7778 u16,u17,u18,u19,u20,u21,u22,u40,u41 465397 true Solanum_nigrum_k1001_c90 0 0.45446074 9 12 2337 u7,u8,u9,u10,u11,u12,u13,u51,u52 465397 true Solanum_nigrum 0 0.46300626 1 1 557 u10 115033 true Sparganium_emersum 1 0.46656966 1 1 432 u11 132649 true Sparganium_emersum 2 0.46350446 1 1 445 u13 172665 true Sparganium_emersum 0 0.44828624 7 12 487.7143 u25,u26,u27,u28,u29,u30,u31 335332 false Spergula_arvensis 0 0.4458264 22 32 3355.818 u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u18,u19,u20,u50,u51,u52,u53,u54 334589 false Spergularia_bocconei 0 0.44665277 19 28 1255.421 u3,u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14,u15,u16,u17,u87,u88,u89,u90 333072 false Spergularia_marina 0 0.38999182 1 1 1243 u12 141744 true Sphagnum_contortum 0 0.39055243 1 1 695 u7 142534 true Sphagnum_girgensohnii 0 0.38999492 1 1 872 u20 141348 true Sphagnum_tenellum 0 0.40867206 1 1 432 u20 105488 true Straminergon_stramineum 0 0.45474955 12 16 607 u33,u34,u35,u36,u37,u38,u39,u40,u41,u42,u43,u44 481411 false Succisa_pratensis 1 0.43737668 1 1 506 u48 64361 true Succisa_pratensis 0 0.4442779 6 8 1678.5 u20,u21,u22,u23,u24,u25 771760 false Syringa_vulgaris 0 0.44767106 9 12 1598.7778 u13,u14,u15,u16,u17,u18,u19,u20,u21 456413 false Tamarix_gallica 0 0.4557281 2 3 289.5 u8,u9 222020 false Tanacetum_parthenium 0 0.45415118 1 1 345 u21 228043 true Tanacetum_vulgare 0 0.46362844 3 4 376.33334 u26,u27,u28 422940 false Thalictrum_minus 0 0.41057503 1 1 225 u7 103489 true Thuidium_tamariscinum 0 0.44033992 24 32 4027.7083 u219,u220,u221,u222,u223,u224,u225,u226,u227,u228,u229,u230,u231,u232,u233,u234,u235,u236,u237,u238,u838,u839,u840,u841 293079 false Torilis_japonica 0 0.46015844 10 14 1498.1 u81,u82,u83,u84,u85,u86,u87,u88,u89,u90 337952 false Tragopogon_pratensis 0 0.41955698 12 16 514.6667 u3,u4,u5,u6,u7,u8,u9,u10,u11,u12,u13,u14 1511433 false Trichophorum_cespitosum 0 0.44351092 1 1 571 u127 51656 true Trifolium_dubium 1 0.44462404 1 1 749 u128 82292 true Trifolium_dubium 2 0.45519584 1 1 1042 u135 183666 true Trifolium_dubium 0 0.46318552 3 4 555.6667 u42,u43,u44 296439 false Trifolium_fragiferum 0 0.45389763 3 4 2073 u1801,u1802,u1803 321896 true Trifolium_occidentale 0 0.44218245 5 7 723.4 u40,u41,u42,u43,u44 286982 false Trifolium_striatum 0 0.4473666 6 8 2352.1667 u192,u193,u194,u195,u196,u197 308677 false Trifolium_subterraneum 0 0.47656614 13 17 1004.1539 u190,u191,u192,u193,u194,u195,u196,u197,u198,u199,u200,u201,u497 310738 false Triglochin_maritima 1 0.48500642 1 1 828 u255 38950 true Triglochin_maritima 0 0.48638278 1 1 275 u34 220713 true Triglochin_palustris 1 0.47868237 1 1 198 u37 132754 true Triglochin_palustris 0 0.4455105 6 8 472.16666 u7,u8,u9,u10,u11,u12 216723 false Tripolium_pannonicum 1 0.4493063 1 1 470 u19 84330 true Tripolium_pannonicum 0 0.45184407 12 16 1404.1666 u76,u77,u78,u79,u80,u81,u82,u83,u84,u85,u86,u198 303483 false Tussilago_farfara 0 0.45015153 1 1 1417 u25 521320 true Ulmus_glabra 0 0.4136162 3 4 707 u32,u33,u34 523275 false Ulmus_minor 0 0.39854282 1 1 867 u18 105547 true Ulota_crispa 0 0.45168412 1 1 1525 u27 242384 true Umbilicus_rupestris 0 0.37745628 12 16 2237.9167 u88,u89,u90,u91,u92,u93,u94,u95,u96,u97,u256,u257 313641 false Urtica_dioica 0 0.3883233 3 4 1231.3334 u83,u84,u85 334764 false Urtica_urens 0 0.45395127 1 1 754 u75 551720 true Vaccinium_vitis_idaea 0 0.44869778 3 4 1258.6666 u12,u13,u14 325752 false Verbascum_nigrum 1 0.45286945 1 1 962 u20 159090 true Verbascum_nigrum 0 0.4490308 3 4 747.6667 u1,u31,u32 318099 false Verbascum_thapsus 1 0.46952763 3 4 505 u30,u224,u225 159163 false Verbascum_thapsus 0 0.45579365 6 8 2151.3333 u5,u6,u7,u8,u9,u10 491677 false Verbena_officinalis 0 0.43969873 3 4 907 u16,u17,u18 340626 false Veronica_anagallis_aquatica 0 0.46141568 3 4 2454.3333 u12,u13,u14 277530 false Veronica_arvensis 0 0.44463867 1 1 830 u27 201946 true Veronica_scutellata 1 0.4377163 1 1 815 u30 134064 true Veronica_scutellata 0 0.44683936 3 4 2164 u20,u21,u22 324799 false Veronica_serpyllifolia 0 0.43483087 6 8 3981.8333 u20,u21,u22,u23,u24,u175 324556 false Veronica_triphyllos 0 0.45387718 3 4 2312.6667 u49,u50,u51 306776 false Veronica_verna 0 0.4647546 3 4 1856 u9,u10,u11 401813 false Vicia_sativa 0 0.4417749 1 1 1274 u45 482146 true Viola_odorata 0 0.454627 3 4 88 u12,u13,u14 120787 false Viscum_album.k1001.s31.c20 1 0.45140448 3 4 104.333336 u17,u18,u19 289094 true Viscum_album.k1001.s31.c20 2 0.46244445 1 1 84 u24 134321 true Viscum_album.k1001.s31.c20 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Life'`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":73,"value":"viewof showLength = {\n const form = html`

Show branch length`;\n const timeout = setTimeout(() => {\n form.i.checked = true;\n form.i.onclick();\n }, 2000);\n form.i.onclick = () => {\n clearTimeout(timeout);\n form.value = form.i.checked;\n form.dispatchEvent(new CustomEvent(\"input\"));\n };\n form.value = false;\n return form;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":30,"value":"$31","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":342,"value":"chart.update(showLength)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":26,"value":"cluster = d3.cluster()\n .size([360, innerRadius])\n .separation((a, b) => 1)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"color = d3\n .scaleOrdinal()\n .domain([\"Non-sedge flowering plants\", \"Sedges\", \"Mosses\"])\n .range(d3.schemeCategory10)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":67,"value":"// Compute the maximum cumulative length of any node in the tree.\nfunction maxLength(d) {\n return d.data.length + (d.children ? d3.max(d.children, maxLength) : 0);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":64,"value":"// Set the radius of each node by recursively summing and scaling the distance from the root.\nfunction setRadius(d, y0, k) {\n d.radius = (y0 += d.data.length) * k;\n if (d.children) d.children.forEach(d => setRadius(d, y0, k));\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":61,"value":"// Set the color of each node by recursively inheriting.\nfunction setColor(d) {\n if (!d.children || d.children.length === 0) {\n // Leaf node\n const name = d.data.name;\n d.group = nameToGroup[name] || null;\n } else {\n const childGroups = new Set();\n d.children.forEach(child => {\n setColor(child);\n if (child.group) childGroups.add(child.group);\n });\n\n // If all children share the same group, assign it to the parent\n if (childGroups.size === 1) {\n d.group = [...childGroups][0];\n } else {\n d.group = null; // Mixed group — do not assign\n }\n }\n\n d.color = d.group ? color(d.group) : (d.parent ? d.parent.color : null);\n}\n","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":119,"value":"function linkVariable(d) {\n return linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":122,"value":"function linkConstant(d) {\n return linkStep(d.source.x, d.source.y, d.target.x, d.target.y);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":116,"value":"function linkExtensionVariable(d) {\n return linkStep(d.target.x, d.target.radius, d.target.x, innerRadius);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":125,"value":"function linkExtensionConstant(d) {\n return linkStep(d.target.x, d.target.y, d.target.x, innerRadius);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":46,"value":"function linkStep(startAngle, startRadius, endAngle, endRadius) {\n const c0 = Math.cos(startAngle = (startAngle - 90) / 180 * Math.PI);\n const s0 = Math.sin(startAngle);\n const c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI);\n const s1 = Math.sin(endAngle);\n return \"M\" + startRadius * c0 + \",\" + startRadius * s0\n + (endAngle === startAngle ? \"\" : \"A\" + startRadius + \",\" + startRadius + \" 0 0 \" + (endAngle > startAngle ? 1 : 0) + \" \" + startRadius * c1 + \",\" + startRadius * s1)\n + \"L\" + endRadius * c1 + \",\" + endRadius * s1;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":92,"value":"legend = (svg) => {\n const g = svg\n .selectAll(\"g\")\n .data(color.domain())\n .join(\"g\")\n .attr(\n \"transform\",\n (d, i) => `translate(${-outerRadius},${-outerRadius + i * 30})`\n );\n\n g.append(\"rect\").attr(\"width\", 24).attr(\"height\", 24).attr(\"fill\", color);\n\n g.append(\"text\")\n .attr(\"x\", 30)\n .attr(\"y\", 9)\n .attr(\"dy\", \"0.5em\")\n .attr(\"font-size\", \"20px\")\n .text((d) => d);\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":280,"value":"function forceUltrametricExtend(tree) {\n // Step 1: Calculate distance from root to each tip\n function tipDepths(node, depth = 0, result = {}) {\n const currentLength = node.length ?? 0;\n const newDepth = depth + currentLength;\n\n if (!node.branchset || node.branchset.length === 0) {\n result[node.name] = newDepth;\n } else {\n node.branchset.forEach((child) => tipDepths(child, newDepth, result));\n }\n return result;\n }\n\n const depths = tipDepths(tree);\n const maxDepth = Math.max(...Object.values(depths));\n\n // Step 2: Extend terminal branches\n function extendTips(node, depth = 0) {\n const currentLength = node.length ?? 0;\n const newDepth = depth + currentLength;\n\n if (!node.branchset || node.branchset.length === 0) {\n // leaf node\n const missing = maxDepth - newDepth;\n node.length = (node.length ?? 0) + missing;\n } else {\n node.branchset.forEach((child) => extendTips(child, newDepth));\n }\n }\n\n extendTips(tree, 0);\n return tree;\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":282,"value":"data = forceUltrametricExtend(data2)","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":38,"value":"data2 = parseNewick(await FileAttachment(\"concatenated.dated.treefile\").text())","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":8,"value":"width = 954","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"outerRadius = width / 2","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"innerRadius = outerRadius - 170","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":34,"value":"// https://github.com/jasondavies/newick.js\nfunction parseNewick(a){for(var e=[],r={},s=a.split(/\\s*(;|\$|\$|,|:)\\s*/),t=0;t d.sp).map(([sp, entries]) => {\n const totalNodes = d3.sum(entries, d => d.node_count);\n return [sp.trim().toLowerCase(), totalNodes];\n })\n);","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":299,"value":"gcMap = {\n const grouped = d3.groups(pdata, (d) => d.sp);\n\n return new Map(\n grouped.map(([sp, entries]) => {\n const totalLen = d3.sum(entries, (d) => d.seq_len);\n const weightedGC = d3.sum(entries, (d) => d.gc * d.seq_len) / totalLen;\n return [sp.trim().toLowerCase(), weightedGC];\n })\n );\n}","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":211,"value":"pdata = d3.tsvParse(polarData, (d) => ({\n si: +d.subgraph_index,\n gc: +d.gc,\n node_count: +d.node_count,\n edge_count: +d.edge_count,\n cov: +d.coverage,\n segs: d.segments.split(\",\"),\n seq_len: +d.total_seq_len,\n is_circular: d.is_circular,\n sp: d.species\n}))","pinned":true,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":208,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W34","stdlib":"1","titling":"auto"}} 30:"$2f:body"