2b:null 2c:["$","title",null,{"children":"lwCoPhylo | Max Brown | Observable"}] 31:Td96,{ const svg = d3.select(nuclear_v_mito); const links = svg.selectAll("path.link"); // datum = label const leftTips = svg.selectAll("circle.tip.left"); // datum has .thisLabel const rightTips = svg.selectAll("circle.tip.right"); // Capture baseline styles once (so we can restore them) links.each(function () { const s = d3.select(this); if (this.__w0 == null) this.__w0 = +s.attr("stroke-width") || 1; if (this.__op0 == null) this.__op0 = +s.attr("stroke-opacity") || 0.6; }); function cacheTipBase(sel) { sel.each(function () { const s = d3.select(this); if (this.__r0 == null) this.__r0 = +s.attr("r") || 2; }); } cacheTipBase(leftTips); cacheTipBase(rightTips); // Tooltip const tip = d3 .select(document.body) .append("div") .style("position", "fixed") .style("pointer-events", "none") .style("background", "rgba(255,255,255,0.96)") .style("border", "1px solid #ccc") .style("padding", "6px 8px") .style("border-radius", "6px") .style("font", "12px/1.3 system-ui, -apple-system, Segoe UI, sans-serif") .style("box-shadow", "0 2px 10px rgba(0,0,0,0.1)") .style("opacity", 0); // Precompute any info you want to show const Ltips = mito_data.data.filter((d) => d.isTip); const Rtips = plastid_data.data.filter((d) => d.isTip); const Lby = new Map(Ltips.map((d) => [d.thisLabel, d])); const Rby = new Map(Rtips.map((d) => [d.thisLabel, d])); function setTip(label, evt) { const L = Lby.get(label), R = Rby.get(label); if (!L || !R) return; const dRank = Math.abs(+L.y1 - +R.y1); tip .html( `

${label}

Δ rank: ${dRank}

${label}

Δ rank: ${dRank}

${label}

Δ rank: ${dRank}

` ) .style("opacity", 1) .style("left", evt.clientX + 12 + "px") .style("top", evt.clientY + 12 + "px"); } function highlight(label) { if (label == null) { // restore all originals links .attr("stroke-opacity", function () { return this.__op0; }) .attr("stroke-width", function () { return this.__w0; }); leftTips.attr("r", function () { return this.__r0; }); rightTips.attr("r", function () { return this.__r0; }); return; } // emphasize hovered label links .attr("stroke-opacity", (d) => (d === label ? 1 : 0.08)) .attr("stroke-width", function (d) { return d === label ? Math.max(2, this.__w0 * 1.8) : Math.max(0.5, this.__w0 * 0.5); }); leftTips.attr("r", function (d) { return d.thisLabel === label ? this.__r0 + 2 : this.__r0; }); rightTips.attr("r", function (d) { return d.thisLabel === label ? this.__r0 + 2 : this.__r0; }); } links .on("mouseenter", (evt, label) => { setTip(label, evt); highlight(label); }) .on("mousemove", (evt, label) => { setTip(label, evt); }) .on("mouseleave", () => { tip.style("opacity", 0); highlight(null); }); function wireTips(sel) { sel .on("mouseenter", (evt, d) => { setTip(d.thisLabel, evt); highlight(d.thisLabel); }) .on("mousemove", (evt, d) => { setTip(d.thisLabel, evt); }) .on("mouseleave", () => { tip.style("opacity", 0); highlight(null); }); } wireTips(leftTips); wireTips(rightTips); chart; // keep visible }34:T1b1e,function cophylo({ left, right, width = 960, height = 600, margin = { top: 20, right: 20, bottom: 20, left: 20 }, gap = 60, stroke = "#777", tipStroke = "black", tipFill = "black", linkStroke = "#999", linkOpacity = 0.5, tipRadius = 1, tipRadiusHighlight = 4, tipRadiusAccessor = null, // (label) => number | falsy linkStrokeWidth = 1, sortLinksByY = true, labelAccessor = (d) => d.thisLabel // customize if needed } = {}) { const EPS = 1e-9; const toHoriz = (d) => Math.abs((d.y1 ?? NaN) - (d.y0 ?? NaN)) < EPS; const toVert = (d) => Math.abs((d.x1 ?? NaN) - (d.x0 ?? NaN)) < EPS; const norm = (tree) => { const data = tree.data ?? []; const horizontal = data.filter(toHoriz); const vertical = tree.vertical_lines && tree.vertical_lines.length ? tree.vertical_lines : data.filter(toVert); // enrich labels/tip flags for (const d of horizontal) { if (d.thisLabel == null) d.thisLabel = labelAccessor(d); if (d.isTip == null) d.isTip = !!d.thisLabel && (d.children?.length ?? 0) === 0; } return { horizontal, vertical }; }; const L = norm(left); const R = norm(right); const innerW = width - margin.left - margin.right; const innerH = height - margin.top - margin.bottom; const leftW = (innerW - gap) / 2; const rightW = (innerW - gap) / 2; const extentX = (H) => d3.extent(H.flatMap((d) => [d.x0, d.x1])); const extentY = (H, V) => d3.extent([ ...H.flatMap((d) => [d.y0, d.y1]), ...V.flatMap((d) => [d.y0, d.y1]) ]); const [lxmin, lxmax] = extentX(L.horizontal); const [lymin, lymax] = extentY(L.horizontal, L.vertical); const [rxmin, rxmax] = extentX(R.horizontal); const [rymin, rymax] = extentY(R.horizontal, R.vertical); const xL = d3.scaleLinear().domain([lxmin, lxmax]).range([0, leftW]); const yL = d3.scaleLinear().domain([lymin, lymax]).range([0, innerH]); const xR = d3.scaleLinear().domain([rxmin, rxmax]).range([0, rightW]); const yR = d3.scaleLinear().domain([rymin, rymax]).range([0, innerH]); const leftTips = L.horizontal.filter( (d) => d.isTip && (d.x1 ?? 0) > (d.x0 ?? 0) ); const rightTips = R.horizontal.filter( (d) => d.isTip && (d.x1 ?? 0) > (d.x0 ?? 0) ); const leftByLabel = new Map(leftTips.map((d) => [d.thisLabel, d])); const rightByLabel = new Map(rightTips.map((d) => [d.thisLabel, d])); let shared = [...leftByLabel.keys()].filter((k) => rightByLabel.has(k)); if (sortLinksByY) { shared.sort((a, b) => { const la = leftByLabel.get(a), lb = leftByLabel.get(b); const ra = rightByLabel.get(a), rb = rightByLabel.get(b); const ya = (yL(la.y1) + yR(ra.y1)) / 2; const yb = (yL(lb.y1) + yR(rb.y1)) / 2; return ya - yb; }); } const leftOriginX = margin.left; const leftOriginY = margin.top; const rightOriginX = margin.left + leftW + gap + rightW; // mirror anchor const rightOriginY = margin.top; const svg = d3 .create("svg") .attr("viewBox", [0, 0, width, height]) // responsive .attr("preserveAspectRatio", "xMidYMid meet") .style("max-width", "100%") .style("height", "auto"); const gRoot = svg.append("g"); const strokeWidth = 1; // LINKS ---------------------------------------------------------------------- const leftPos = new Map( leftTips.map((d) => [ d.thisLabel, { x: leftOriginX + xL(d.x1), y: leftOriginY + yL(d.y1) } ]) ); const rightPos = new Map( rightTips.map((d) => [ d.thisLabel, { x: rightOriginX - xR(d.x1), y: rightOriginY + yR(d.y1) } // mirrored x ]) ); const linkPath = (L, R) => { const midX = (L.x + R.x) / 2; return `M${L.x},${L.y} C${midX},${L.y} ${midX},${R.y} ${R.x},${R.y}`; }; gRoot .append("g") .attr("class", "cophylo-links") .selectAll("path.link") .data(shared) .join("path") .attr("class", "link") .attr("d", (label) => { const Lp = leftPos.get(label), Rp = rightPos.get(label); return Lp && Rp ? linkPath(Lp, Rp) : null; }) .attr("fill", "none") .attr( "stroke", typeof linkStroke === "function" ? (d) => linkStroke(d) : linkStroke ) .attr("stroke-opacity", linkOpacity) .attr( "stroke-width", typeof linkStrokeWidth === "function" ? (d) => linkStrokeWidth(d) : linkStrokeWidth ); // LEFT ----------------------------------------------------------------------- const gLeft = gRoot .append("g") .attr("transform", `translate(${leftOriginX},${leftOriginY})`); gLeft .append("g") .selectAll("line.h") .data(L.horizontal) .join("line") .attr("x1", (d) => xL(d.x0) - strokeWidth / 2) .attr("y1", (d) => yL(d.y0)) .attr("x2", (d) => xL(d.x1) - strokeWidth / 2) .attr("y2", (d) => yL(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gLeft .append("g") .selectAll("line.v") .data(L.vertical) .join("line") .attr("x1", (d) => xL(d.x0)) .attr("y1", (d) => yL(d.y0)) .attr("x2", (d) => xL(d.x1)) .attr("y2", (d) => yL(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gLeft .append("g") .selectAll("circle.tip") .data(leftTips) .join("circle") .attr("class", "tip left") .attr("r", (d) => { const v = tipRadiusAccessor ? +tipRadiusAccessor(d.thisLabel) : 0; return v > 0 ? tipRadiusHighlight : tipRadius; }) .attr("cx", (d) => xL(d.x1)) .attr("cy", (d) => yL(d.y1)) .attr("fill", tipFill) .attr("stroke", tipStroke); // RIGHT (mirrored) ----------------------------------------------------------- const gRight = gRoot .append("g") .attr( "transform", `translate(${rightOriginX},${rightOriginY}) scale(-1,1)` ); gRight .append("g") .selectAll("line.h") .data(R.horizontal) .join("line") .attr("x1", (d) => xR(d.x0) - strokeWidth / 2) .attr("y1", (d) => yR(d.y0)) .attr("x2", (d) => xR(d.x1) - strokeWidth / 2) .attr("y2", (d) => yR(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gRight .append("g") .selectAll("line.v") .data(R.vertical) .join("line") .attr("x1", (d) => xR(d.x0)) .attr("y1", (d) => yR(d.y0)) .attr("x2", (d) => xR(d.x1)) .attr("y2", (d) => yR(d.y1)) .attr("stroke", stroke) .attr("stroke-width", strokeWidth); gRight .append("g") .selectAll("circle.tip") .data(rightTips) .join("circle") .attr("class", "tip right") .attr("r", (d) => { const v = tipRadiusAccessor ? +tipRadiusAccessor(d.thisLabel) : 0; return v > 0 ? tipRadiusHighlight : tipRadius; }) .attr("cx", (d) => xR(d.x1)) .attr("cy", (d) => yR(d.y1)) .attr("fill", tipFill) .attr("stroke", tipStroke); return Object.assign(svg.node(), { svg }); }35:T36a9,mito = `((((((((((((Myriophyllum_alterniflorum:46.742686,Umbilicus_rupestris:46.742686)99.8/100:5.127168,((Ribes_rubrum:1.962206,Ribes_uva_crispa:1.962206)100/100:26.164065,Saxifraga_aizoides:28.12627)100/100:23.743584)99.8/100:72.945247,((((((((((Acaena_ovalifolia:132.567471,(((Rosa_agrestis:0.107324,Rosa_canina:0.107324)98.3/100:0.670103,Rosa_spinosissima:0.777427)78.7/100:0.605239,Rosa_rugosa:1.382666)100/100:131.184805):0.288079,((Comarum_palustre:8.201362,(Fragaria_moschata:0.594634,Fragaria_vesca:0.594634)100/100:7.606728)100/100:18.892044,(Potentilla_anserina:13.529333,(Potentilla_indica:9.09961,Potentilla_sterilis:9.09961)99.2/100:4.429722)100/100:13.564074)100/100:105.185986)10.8/98:0.663946,(Rubus_caesius:4.966326,Rubus_idaeus:4.966326)100/100:126.649119)99.9/100:0.299208,(Geum_rivale:0.003397,Geum_urbanum:0.003397)100/100:131.312841)54.2/100:0.969928,Filipendula_ulmaria:130.346309)89.3/99:2.713717,(Dryas_octopetala:18.678045,(((Crataegus_laevigata:0.487985,Pyrus_communis:0.487985)35.8/100:0.094195,(Malus_domestica:0.153464,(Malus_x_robusta:0.001684,Malus_sylvestris:0.001684)0/100:0.151781)96.5/100:0.428715)100/100:10.428935,Prunus_padus:11.011115)100/100:7.66693)79.5/100:108.954548)100/100:2.00906,(Frangula_alnus:56.459539,((Humulus_lupulus:44.855982,(Parietaria_judaica:39.043823,(Urtica_dioica:3.010487,Urtica_urens:3.010487)100/100:36.033336)99.6/100:5.812158)99.9/100:2.798265,(Ulmus_glabra:0.00208,Ulmus_minor:0.00208)100/100:47.652167)100/100:8.805292)100/100:69.163994)100/100:0.398336,(((((Alnus_glutinosa:0.060906,Alnus_incana:0.060906)99.9/100:3.153717,Corylus_avellana:3.214623)100/100:10.548469,Myrica_gale:13.763092)98/100:26.71957,(Fagus_sylvatica:37.8,(Quercus_ilex:3.396133,(Quercus_petraea:0.132244,Quercus_robur:0.132244)99.7/100:3.263889)100/100:34.403867)100/100:2.682662)100/100:26.226687,(((Astragalus_alpinus:1.453175,Astragalus_glycyphyllos:1.453175)100/100:11.755881,((Lathyrus_linifolius:4.497537,Vicia_sativa:4.497537)100/100:2.543125,(((Trifolium_dubium:4.855476,(((Trifolium_fragiferum:1.377587,Trifolium_occidentale:1.377587)97.2/100:1.019396,Trifolium_subterraneum:2.396983)88.6/100:0.307959,Trifolium_striatum:2.704942)100/100:2.150534)96.8/100:1.244862,(Medicago_arabica:1.641175,Medicago_lupulina:1.641175)100/100:4.459163)85.6/99:0.320061,Ononis_reclinata:6.4204)91.8/99:0.620262)100/100:6.168394)100/100:7.805552,Laburnum_anagyroides:21.014609)100/100:45.694741)1.4/32:58.515847)99.6/100:0.225197,(((Euonymus_europaeus:73.843944,((((Euphorbia_lathyris:14.091356,Euphorbia_peplus:14.091356)96/100:3.303459,Euphorbia_maculata:17.394816)100/100:32.252637,Mercurialis_annua:49.647453)100/100:18.826744,(((Hypericum_androsaemum:3.220125,(Hypericum_hirsutum:1.232081,Hypericum_pulchrum:1.232081)100/100:1.988043)100/100:62.206134,(Populus_tremula:48.805882,(Populus_nigra:48.5,(Salix_caprea:1.860413,((Salix_cinerea:0.000275,Salix_viminalis:0.000275):0.001566,Salix_repens:0.001841)0/100:1.858572)100/100:46.639587)94.2/100:0.305882)100/100:16.620377)63.6/100:2.091493,Viola_odorata:67.517752)94/99:0.956444)100/100:5.369748)15.7/71:0.894639,(((Acer_campestre:10.982836,Aesculus_hippocastanum:10.982836)100/100:10.0394,Ailanthus_altissima:21.022236)100/100:41.981478,(((((Arabidopsis_thaliana:4.616691,Lepidium_didymum:4.616691)80.1/100:0.561633,(Barbarea_vulgaris:2.93784,((Cardamine_flexuosa:0.043824,Cardamine_hirsuta:0.043824)100/100:2.652183,Nasturtium_officinale:2.696007)84/100:0.241833)100/100:2.240484)99.4/100:2.220465,((Arabis_hirsuta:3.357337,(Draba_incana:2.928572,Draba_verna:2.928572)95.9/100:0.428765)99.8/100:2.34543,Brassica_nigra:5.702767)95.8/100:1.696021)84.9/100:5.513388,Matthiola_sinuata:12.912177)100/100:47.526112,((Hibiscus_tridactylites:1.577021,Hibiscus_verdcourtii:1.577021)100/100:32.322979,Malva_neglecta:33.9)100/100:26.538288)94.6/100:2.565426)99.9/100:11.734869)98.8/100:25.403309,((Chamaenerion_angustifolium:6.421446,Epilobium_hirsutum:6.421446)100/100:86.66859,((Erodium_maritimum:3.666492,Erodium_moschatum:3.666492)99.2/100:4.841662,(Geranium_rotundifolium:3.288658,Geranium_molle:3.288658)100/100:5.219496)100/100:84.581882)98.8/100:7.051856)61.1/75:24.858108)98.4/99:0.167491,((((((Agrostemma_githago:14.308749,(Arenaria_serpyllifolia:6.869318,Moehringia_trinervia:6.869318)100/100:7.439431)90.6/100:1.848982,(Spergula_arvensis:10.399378,(Spergularia_bocconei:0.051883,Spergularia_marina:0.051883)100/100:10.347495)100/100:5.758353)100/100:16.72766,((Blitum_bonus_henricus:7.925221,Chenopodium_album:7.925221)97.6/100:4.700352,Salicornia_ramosissima:12.625572)100/100:20.259819)100/100:37.319844,Tamarix_gallica:70.205236)47.7/98:14.775161,(((Fallopia_convolvulus:66,(Polygonum_aviculare:1.805023,Polygonum_maritimum:1.805023)100/100:64.194977)8.3/80:0.329666,Oxyria_digyna:66.329666)99.7/100:1.3533,Persicaria_maculosa:67.682966)100/100:17.297431)100/100:36.067572,((((((Calystegia_soldanella:1.940441,Convolvulus_arvensis:1.940441)100/100:45.896215,(Solanum_dulcamara:33.9,Solanum_nigrum:33.9)100/100:13.936656)100/100:7.048203,(((Quercus_cerris:38.60298,(Sherardia_arvensis:3.155087,(Cruciata_laevipes:1.760754,(Galium_aparine:1.124346,Galium_uliginosum:1.124346)96.7/100:0.636408)99.9/100:1.394333)100/100:35.447893)100/100:11.316074,Pentaglottis_sempervirens:49.919054)61.8/75:2.597347,((((((Ajuga_chamaepitys:27.183752,((((Ballota_nigra:2.891649,(Lamium_amplexicaule:0.97501,Lamium_purpureum:0.97501)99.4/100:1.916639)63.9/78:0.862517,Melittis_melissophyllum:3.754166)66.1/78:1.57549,Galeopsis_tetrahit:5.329656)100/100:19.668968,(Scutellaria_galericulata:0.153163,Scutellaria_minor:0.153163)100/100:24.845462)94/100:2.185127)97.7/100:0.636248,(Lycopus_europaeus:7.448161,Prunella_vulgaris:7.448161)100/100:20.371839)100/100:2.837992,((Euphrasia_confusa:5.575948,Rhinanthus_minor:5.575948)87.7/100:2.299295,Melampyrum_sylvaticum:7.875243)100/100:22.782749)99.1/100:0.925666,(Verbena_officinalis:15.120211,(Verbascum_nigrum:0.053499,Verbascum_thapsus:0.053499)100/100:15.066712)100/100:16.463447)99.8/100:1.55925,((Callitriche_obtusangula:29.70762,((Veronica_scutellata:5.446113,(Veronica_anagallis_aquatica:2.355438,Veronica_serpyllifolia:2.355438)100/100:3.090675)91.7/100:1.071835,((Veronica_arvensis:2.7782,Veronica_verna:2.7782)97.9/100:1.627799,Veronica_triphyllos:4.405999)99.4/100:2.111948)100/100:23.189672)99.9/100:2.100654,((Linaria_vulgaris:8.589782,Misopates_orontium:8.589782)99/100:3.176866,Cymbalaria_muralis:11.766648)99.7/100:20.041626)98.8/100:1.334634)100/100:6.1832,(Ligustrum_vulgare:2.75075,Syringa_vulgaris:2.75075)100/100:36.575359)100/100:13.190292)49.7/74:2.368458)100/100:9.336966,((((((((((Tanacetum_parthenium:2.21741,((Matricaria_chamomilla:0.293511,Matricaria_discoidea:0.293511)99.8/100:0.65852,Tanacetum_vulgare:0.952031)99.8/100:1.265379)100/100:6.491948,Pulicaria_dysenterica:8.709359)92.2/100:0.812925,(((((Jacobaea_maritima:0.000611,Jacobaea_vulgaris:0.000611)99.1/100:1.022296,Senecio_sylvaticus:1.022907)91.8/99:0.50755,((Petasites_albus:0.274754,Petasites_hybridus:0.274754)60.2/100:0.081725,Tussilago_farfara:0.356479)91.2/100:1.173977)100/100:3.929565,Calendula_officinalis:5.460022)3.6/57:0.695487,(((Filago_lutescens:0.320685,(Logfia_minima:0.260867,Gnaphalium_supinum:0.260867)77.4/100:0.059818)99.5/100:1.609844,(Pseudognaphalium_luteoalbum:1.602163,Gnaphalium_uliginosum:1.602163)88.7/100:0.328366)100/100:3.813782,(Tripolium_pannonicum:0.669932,Galatella_linosyris:0.669932)100/100:5.074378)78.7/99:0.411199)83.5/98:3.366774)86.9/100:37.937717,(Lapsana_communis:12.048601,Tragopogon_pratensis:12.048601)99.9/100:35.411399)95.5/100:0.187875,Carlina_vulgaris:47.647875)61.3/99:0.126479,((Carduus_nutans:1.195174,Cirsium_eriophorum:1.195174)78.2/100:0.400174,Arctium_minus:1.595348)100/100:46.179006)100/100:7.507457,(Jasione_montana:26.002716,(Lobelia_dortmanna:7.943033,Lobelia_urens:7.943033)100/100:18.059683)100/100:29.279095)100/100:3.657685,((Hedera_helix:21.509465,Hydrocotyle_vulgaris:21.509465)99.8/100:31.802071,(Ammi_majus:41.2,Torilis_japonica:41.2)100/100:12.111535)100/100:5.62796)62.4/96:0.630218,(Sambucus_nigra:19.03286,Succisa_pratensis:19.03286)100/100:40.536853)98/100:1.429052,Ilex_aquifolium:60.998765)86.9/99:3.22306)95.4/98:49.752368,(((Calluna_vulgaris:66,Vaccinium_vitis_idaea:66)100/100:45.001211,(((Primula_veris:0.246904,Primula_vulgaris:0.246904)100/100:28.096421,Samolus_valerandi:28.343326)100/100:82.635516,Viscum_album:110.978841)0/36:0.02237)39.8/37:0.66459,(Impatiens_glandulifera:0.687649,Impatiens_parviflora:0.687649)100/100:110.978152)100/100:2.308391)20.3/45:0.433102,Cornus_suecica:114.407295)100/100:6.640673)64.8/77:3.784541)99.8/91:0.017408)37.3/76:0.359493,Buxus_sempervirens:124.455608)100/100:0.265133,((((Ranunculus_sardous:4.634709,Ranunculus_sceleratus:4.634709)100/100:29.770725,Adonis_annua:34.405434)99.9/100:21.594566,(Aquilegia_vulgaris:14.326715,Thalictrum_minus:14.326715)100/100:41.673285)100/100:9.562751,Berberis_vulgaris:65.562751)100/100:58.627725)100/100:0.191776,((Lemna_minuta:104.857141,((Alisma_plantago_aquatica:40.068159,Aponogeton_distachyos:40.068159)60.8/100:3.073828,(Potamogeton_natans:29.952021,(Triglochin_maritima:1.319346,Triglochin_palustris:1.319346)100/100:28.632675)100/100:13.189966)100/100:61.715154)97.8/100:8.142859,(((((((Bromus_sterilis:10.87137,(Poa_chaixii:7.223609,Polypogon_viridis:7.223609)99.8/100:3.64776)100/100:18.262838,Leersia_oryzoides:29.134207)17.1/100:1.305793,(Digitaria_sanguinalis:10.916558,Phragmites_australis:10.916558)99.2/100:19.523442)100/100:44.280313,((((((((Carex_acutiformis:1.210612,Carex_nigra:1.210612)97.2/100:2.237738,(Carex_caryophyllea:3.36326,Carex_depauperata:3.36326)75.5/99:0.08509)93.8/100:0.572049,((Carex_sylvatica:2.871951,Carex_pendula:2.871951)96.5/100:0.96879,(Carex_laevigata:2.94008,(Carex_distans:2.645698,Carex_extensa:2.645698)61/100:0.294382)100/100:0.900661)88.8/99:0.179658)41.9/98:0.099925,((Carex_hirta:0.68274,Carex_riparia:0.68274)83.8/96:0.543448,Carex_rostrata:1.226188)99.4/100:2.894136)100/100:4.315327,(Carex_arenaria:2.106747,Carex_divulsa:2.106747)100/100:6.328904)100/100:9.609864,(Trichophorum_cespitosum:14.893583,(Eriophorum_vaginatum:6.488387,Scirpus_sylvaticus:6.488387)100/100:8.405196)50.9/98:3.151932)100/100:13.438233,((Cyperus_fuscus:20.74179,(Schoenoplectus_triqueter:1.386569,Schoenoplectus_lacustris:1.386569)100/100:19.355221)100/100:7.532122,Eleocharis_quinqueflora:28.273912)99.9/100:3.209836)100/100:22.218485,((Juncus_effusus:8.143771,Juncus_squarrosus:8.143771)100/100:7.694315,(Luzula_pallescens:1.056958,Luzula_sylvatica:1.056958)100/100:14.781128)100/100:37.864147)100/100:21.01808)99.7/100:3.845595,Sparganium_emersum:78.565908)100/100:7.732204,Narthecium_ossifragum:86.298112)17.2/89:1.777351,Iris_foetidissima:88.075462)100/100:24.924538)100/100:10.9987)97.8/100:4.278266,(Ginkgo_biloba:87.52973,((juniperus_communis:19.936366,taxus_baccata:19.936366)100/100:52.161518,pinus_sylvestris:72.097885)99.9/100:15.431846)100/100:32.190703)100/100:11.99612,((Selaginella_selaginoides:99.417465,((((Adiantum_capillus_veneris:42.601225,Pteridium_aquilinum:42.601225)2.6/54:2.910135,((Asplenium_adiantum_nigrum:11.482696,((Asplenium_ceterach:4.06413,Asplenium_scolopendrium:4.06413)100/100:6.782248,(Asplenium_marinum:8.942474,(Asplenium_trichomanes:6.170625,Asplenium_viride:6.170625)99.9/100:2.771848)99/100:1.903904)83.5/99:0.636318)100/100:22.288732,((((Cystopteris_fragilis:2.921477,Cystopteris_montana:2.921477)99.8/100:3.255091,Gymnocarpium_robertianum:6.176568)100/100:10.30901,(((Onoclea_sensibilis:6.576957,Struthiopteris_spicant:6.576957)94.8/100:2.020417,Woodsia_ilvensis:8.597374)95.9/100:3.09851,(Thelypteris_palustris:8.278641,Phegopteris_connectilis:8.278641)99.4/100:3.417243)99.5/100:4.789694)91/100:11.661747,((((Dryopteris_borreri:0.00142,Dryopteris_filix_mas:0.00142)95.5/100:7.791637,Dryopteris_dilatata:7.793057)98.3/100:4.754299,(Polystichum_lonchitis:8.954783,Polystichum_setiferum:8.954783)100/100:3.592572)100/100:6.29863,Polypodium_vulgare:18.845985)100/100:9.301339)38.6/77:5.624103)100/100:11.739933)100/100:12.075749,(Azolla_filiculoides:43.561657,Pilularia_globulifera:43.561657)86.2/98:14.025452)100/100:21.6898,Vandenboschia_speciosa:79.27691)95.8/100:20.140555)85/88:4.099067,((((Equisetum_sylvaticum:0.000211,Equisetum_arvense:0.000211):0.000845,Equisetum_pratense:0.001057)0/92:0.002901,Equisetum_fluviatile:0.003958)67.3/100:36.996042,Equisetum_telmateia:37)100/100:66.516532)100/89:4.207782)100/100:24.334248,(Huperzia_selago:25.266492,Lycopodium_clavatum:25.266492)100/100:58.123574)100/89:14.125242,((((((((((Antitrichia_curtipendula:2.447692,Climacium_dendroides:2.447692)97.1/100:1.826342,(Cratoneuron_filicinum:3.358389,Thuidium_tamariscinum:3.358389)89.5/100:0.915644)0/96:0.001477,Rhytidiadelphus_loreus:4.27551)60.7/97:0.481593,(((Calliergon_cordifolium:0.707883,Straminergon_stramineum:0.707883)99.4/100:3.20307,(Hyocomium_armoricum:3.363665,((Pseudoscleropodium_purum:0.812044,Rhynchostegium_megapolitanum:0.812044)91/100:1.186123,Rhynchostegiella_tenella:1.998168)100/100:1.365497)90.2/99:0.547288)79/100:0.544168,(((Heterocladium_heteropterum:2.859549,Neckera_pumila:2.859549)91.4/100:1.079764,Isothecium_myosuroides:3.939313)70.9/76:0.265973,Hypnum_cupressiforme:4.205286)86.5/58:0.249835)86.7/58:0.301982)95.4/100:0.729419,((Orthothecium_rufescens:4.199263,Plagiothecium_denticulatum:4.199263)92.3/100:0.923685,Pseudotaxiphyllum_elegans:5.122948)86.8/84:0.363574)78.2/100:0.672876,Isopterygiella_pulchella:6.159398)100/100:9.81889,Ulota_crispa:15.978288)100/100:7.481866,Bryoerythrophyllum_caledonicum:23.460154)100/100:10.35984,(Polytrichastrum_sexangulare:2.650781,(Polytrichum_commune:1.884972,Polytrichum_formosum:1.884972)94.5/100:0.765808)100/100:31.169213)100/100:12.376562,((Sphagnum_contortum:1.37586,Sphagnum_tenellum:1.37586)91.4/100:0.468597,Sphagnum_girgensohnii:1.844457)100/100:44.352098)100/100:23.068268)100/100:49.658814,Lunularia_cruciata:19.60601)100/100:0,Herbertus_hutchinsiae:19.60601)Root; `36:T36d9,plastid = `(((((((((((((Myriophyllum_alterniflorum:61.363517,Umbilicus_rupestris:61.363517)100/100:10.258805,((Ribes_rubrum:2.93894,Ribes_uva_crispa:2.93894)100/100:43.95497,Saxifraga_aizoides:46.89391)100/100:24.728412)100/100:42.597955,(((((((((((Acaena_ovalifolia:133.646108,(((Rosa_agrestis:0.534566,Rosa_canina:0.534566)100/100:1.69734,(Rosa_spinosissima:1.023443,Rosa_rugosa:1.023443)100/100:1.208462)100/100:15.026756,((Comarum_palustre:6.291973,(Fragaria_moschata:0.088978,Fragaria_vesca:0.088978)100/100:6.202995)100/100:7.00356,(Potentilla_anserina:10.150512,(Potentilla_indica:5.024997,Potentilla_sterilis:5.024997)100/100:5.125515)100/100:3.145021)100/100:3.963129)28/93:116.387446):1.467999,(Rubus_caesius:5.435343,Rubus_idaeus:5.435343)100/100:126.742765)100/100:0.223865,(Geum_rivale:0.033339,Geum_urbanum:0.033339)100/100:131.920905)92.9/99:1.252374,Filipendula_ulmaria:130.701869)100/100:1.893402,Dryas_octopetala:128.808466)100/100:0.136241,((Crataegus_laevigata:1.539809,(Pyrus_communis:1.354791,((Malus_domestica:0.031691,Malus_x_robusta:0.031691)100/100:0.150819,Malus_sylvestris:0.18251)100/100:1.172281)75.4/100:0.185018)100/100:18.561784,Prunus_padus:20.101594)100/100:108.570632)97/99:1.737629,(Frangula_alnus:60.70695,((Humulus_lupulus:43.586852,(Parietaria_judaica:35.469835,(Urtica_dioica:9.972251,Urtica_urens:9.972251)100/100:25.497584)100/100:8.117017)100/100:8.867477,(Ulmus_glabra:0.016665,Ulmus_minor:0.016665)100/100:52.437664)100/100:8.25262)100/100:66.227647)100/100:1.012366,((((Alnus_glutinosa:0.080417,Alnus_incana:0.080417)100/100:8.949685,Corylus_avellana:9.030101)100/100:12.695531,Myrica_gale:21.725632)100/100:24.338055,(Fagus_sylvatica:37.8,(Quercus_ilex:1.964928,((Quercus_petraea:0.008552,(Quercus_robur:0.00053,Tanacetum_parthenium:0.00053)75.6/100:0.008022)100/100:1.729885,Quercus_cerris:1.738437)95.6/100:0.226491)100/100:35.835072)100/100:8.263688)100/100:79.858543)100/100:0.127764,(((Astragalus_alpinus:6.719205,Astragalus_glycyphyllos:6.719205)100/100:30.541637,(((Lathyrus_linifolius:18.848132,Vicia_sativa:18.848132)100/100:9.985798,(Trifolium_dubium:21.661576,((Trifolium_fragiferum:7.908704,Trifolium_occidentale:7.908704)100/100:3.778072,(Trifolium_subterraneum:9.100318,Trifolium_striatum:9.100318)100/100:2.586458)100/100:9.9748)100/100:7.172355)100/100:0.784244,((Medicago_arabica:13.268892,Medicago_lupulina:13.268892)100/100:14.462167,Ononis_reclinata:27.731059)99.8/100:1.887116)100/100:7.642668)100/100:18.739158,Laburnum_anagyroides:56)100/100:69.794467)98.6/99:0.495065,(Euonymus_europaeus:107.154692,((Hypericum_androsaemum:13.29281,(Hypericum_hirsutum:6.860674,Hypericum_pulchrum:6.860674)100/100:6.432136)100/100:72.780484,((((Euphorbia_lathyris:12.383339,Euphorbia_peplus:12.383339)100/100:5.265442,Euphorbia_maculata:17.648782)100/100:26.421876,Mercurialis_annua:44.070658)100/100:33.759137,(((Populus_tremula:1.034544,Populus_nigra:1.034544)100/100:47.465456,(Salix_cinerea:0.118017,(Salix_caprea:0.078338,(Salix_viminalis:0.077575,Salix_repens:0.077575)0/98:0.000762)79.8/99:0.03968)100/100:48.381983)100/100:21.432492,Viola_odorata:69.932492)100/100:7.897302)24/97:8.2435)100/100:21.081397)100/100:18.14471)100/100:0.299402,((((Acer_campestre:14.586313,Aesculus_hippocastanum:14.586313)100/100:20.685204,Ailanthus_altissima:35.271516)100/100:42.640829,(((((Arabidopsis_thaliana:10.45902,Lepidium_didymum:10.45902)47.3/100:0.462266,(Barbarea_vulgaris:8.648753,((Cardamine_flexuosa:0.193731,Cardamine_hirsuta:0.193731)100/100:6.494676,Nasturtium_officinale:6.688408)100/100:1.960345)100/100:2.272534)100/100:3.040794,((Arabis_hirsuta:9.158835,(Draba_incana:6.378267,Draba_verna:6.378267)100/100:2.780568)100/100:3.713735,Brassica_nigra:12.87257)100/100:1.08951)66.7/100:0.749933,Matthiola_sinuata:14.712014)100/100:56.932561,((Hibiscus_tridactylites:2.498,Hibiscus_verdcourtii:2.498)100/100:31.402,Malva_neglecta:33.9)100/100:37.744575)100/100:6.26777)100/100:31.837893,((Chamaenerion_angustifolium:9.616184,Epilobium_hirsutum:9.616184)100/100:94.447494,((Erodium_maritimum:5.984251,Erodium_moschatum:5.984251)100/100:22.426495,(Geranium_rotundifolium:13.702964,Geranium_molle:13.702964)100/100:14.707782)100/100:75.652933)100/100:5.68656)100/100:15.249762)100/100:10.779723)100/100:1.220277,((((((Agrostemma_githago:28.290144,(Arenaria_serpyllifolia:13.178734,Moehringia_trinervia:13.178734)100/100:15.111409)100/100:2.172375,(Spergula_arvensis:20.211652,(Spergularia_bocconei:0.105461,Spergularia_marina:0.105461)100/100:20.106191)100/100:10.250867)100/100:23.278422,((Blitum_bonus_henricus:21.793091,Chenopodium_album:21.793091)100/100:11.991963,Salicornia_ramosissima:33.785054)100/100:19.955887)100/100:39.354881,(Tamarix_gallica:90.384203,(((Fallopia_convolvulus:66,(Polygonum_aviculare:0.97901,Polygonum_maritimum:0.97901)100/100:65.02099)100/100:2.001592,Oxyria_digyna:68.001592)100/100:1.67231,Persicaria_maculosa:69.673902)100/100:20.710301)100/100:2.711619)100/100:15.344242,(((((((Calystegia_soldanella:3.579855,Convolvulus_arvensis:3.579855)100/100:52.707426,(Solanum_dulcamara:33.9,Solanum_nigrum:33.9)100/100:22.387282)100/100:8.171368,(((Sherardia_arvensis:10.071077,Cruciata_laevipes:10.071077)99/100:0.718559,(Galium_aparine:5.820074,Galium_uliginosum:5.820074)100/100:4.969561)100/100:51.291017,Pentaglottis_sempervirens:62.080652)97.7/100:2.377997)25.4/100:0.626141,(((((((Ajuga_chamaepitys:25.004157,(((Ballota_nigra:7.804722,(Lamium_amplexicaule:3.755921,Lamium_purpureum:3.755921)100/100:4.048801)100/100:2.601233,(Melittis_melissophyllum:9.244408,Galeopsis_tetrahit:9.244408)100/100:1.161547)100/100:10.713997,(Scutellaria_galericulata:0.786469,Scutellaria_minor:0.786469)100/100:20.333482)100/100:3.884206)100/100:2.815843,((Lycopus_europaeus:18.816154,Prunella_vulgaris:18.816154)100/100:3.323987,Matricaria_chamomilla:22.14014)100/100:5.67986)100/100:6.261458,((Euphrasia_confusa:16.881987,Rhinanthus_minor:16.881987)100/100:1.944142,Melampyrum_sylvaticum:18.826129)100/100:15.255329)99.6/100:0.61099,Verbena_officinalis:34.692448)100/100:0.732863,(Verbascum_nigrum:0.400608,Verbascum_thapsus:0.400608)100/100:35.024703)100/100:1.036221,((Callitriche_obtusangula:29.907273,(Veronica_scutellata:14.606252,((Veronica_anagallis_aquatica:7.621736,Veronica_serpyllifolia:7.621736)100/100:6.508974,((Veronica_arvensis:7.248243,Veronica_verna:7.248243)100/100:5.236178,Veronica_triphyllos:12.48442)100/100:1.646289)95.8/100:0.475542)100/100:15.301021)100/100:2.559923,((Linaria_vulgaris:17.181979,Misopates_orontium:17.181979)100/100:3.776054,Cymbalaria_muralis:20.958033)100/100:11.509162)100/100:3.994336)100/100:8.051488,(Ligustrum_vulgare:10.945746,Syringa_vulgaris:10.945746)100/100:33.567273)100/100:20.571771)100/100:14.17106,((((((Pulicaria_dysenterica:17.692358,((((Jacobaea_maritima:0.170628,Jacobaea_vulgaris:0.170628)100/100:2.866335,Senecio_sylvaticus:3.036963)100/100:2.563779,((Petasites_albus:0.699432,Petasites_hybridus:0.699432)99.6/100:1.822047,Tussilago_farfara:2.521478)100/100:3.079264)100/100:11.642032,(Calendula_officinalis:15.899167,(((Matricaria_discoidea:1.883357,Tanacetum_vulgare:1.883357)100/100:12.813453,((((Filago_lutescens:2.051182,Logfia_minima:2.051182)99.5/100:0.233034,Gnaphalium_supinum:2.284216)100/100:1.092209,Pseudognaphalium_luteoalbum:3.376425)100/100:0.832552,Gnaphalium_uliginosum:4.208977)100/100:10.487833)55.9/100:0.731104,(Tripolium_pannonicum:2.031951,Galatella_linosyris:2.031951)100/100:13.395964)83.4/100:0.471253)100/100:1.343607)60.1/100:0.449584)100/100:29.767642,(Lapsana_communis:19.616004,Tragopogon_pratensis:19.616004)100/100:27.843996)100/100:0.744442,(Carlina_vulgaris:27.231522,(Carduus_nutans:20.1186,Cirsium_eriophorum:20.1186)100/96:7.112921)100/96:20.97292)100/100:20.815525,(Jasione_montana:50.514465,(Lobelia_dortmanna:16.881913,Lobelia_urens:16.881913)100/100:33.632552)100/100:18.505502)100/100:4.421019,((Sambucus_nigra:57.517588,Succisa_pratensis:57.517588)100/100:10.981893,((Hedera_helix:23.895474,Hydrocotyle_vulgaris:23.895474)100/100:32.401643,((Ammi_majus:41.2,Torilis_japonica:41.2)100/100:6.755728,Lemna_minuta:47.955728)100/100:8.341389)100/100:12.202365)99.9/100:4.941505)100/100:2.860351,Ilex_aquifolium:76.301337)100/100:2.954513)100/100:10.224346,(((Calluna_vulgaris:66,Vaccinium_vitis_idaea:66)100/100:17.653826,((Primula_veris:4.051045,Primula_vulgaris:4.051045)100/100:54.432474,Samolus_valerandi:58.483519)100/100:25.170307)99.6/100:1.041034,(Impatiens_glandulifera:4.57351,Impatiens_parviflora:4.57351)100/100:80.12135)100/100:4.785337)99.7/100:1.057205,Cornus_suecica:90.537402)100/100:17.902662)100/100:2.929353,Viscum_album:111.369417)99.5/100:1.630583)100/100:0.655197,Buxus_sempervirens:112.344803)100/100:0.210465,(((Ranunculus_sardous:13.020693,Ranunculus_sceleratus:13.020693)100/100:44.350912,(Adonis_annua:56,(Aquilegia_vulgaris:19.005715,Thalictrum_minus:19.005715)100/100:36.994285)50.1/97:1.371605)100/100:23.370154,Berberis_vulgaris:80.741759)100/100:31.39258)100/100:0.407274,((Arctium_minus:61.330721,(Alisma_plantago_aquatica:49.787628,(Aponogeton_distachyos:44.508466,(Potamogeton_natans:35.699754,(Triglochin_maritima:2.813521,Triglochin_palustris:2.813521)100/100:32.886232)100/100:8.808712)100/100:5.279162)100/100:11.543093)100/100:34.822361,((((((((Bromus_sterilis:10.731085,Poa_chaixii:10.731085)100/100:3.539842,Polypogon_viridis:14.270927)100/100:13.686918,Leersia_oryzoides:27.957844)98.2/100:2.482156,(Digitaria_sanguinalis:14.387076,Phragmites_australis:14.387076)100/100:16.052924)100/100:49.471701,(((((((Carex_caryophyllea:6.988021,(((Carex_acutiformis:4.393076,Carex_nigra:4.393076)99.3/100:0.344776,((Carex_sylvatica:3.773394,Carex_laevigata:3.773394)99.8/87:0.448946,Carex_pendula:4.22234)98.4/83:0.515513)100/100:1.728049,(Carex_distans:2.877016,Carex_extensa:2.877016)100/100:3.588885)100/100:0.52212)100/100:0.475314,(Carex_depauperata:5.757205,(Carex_hirta:1.414105,(Carex_riparia:1.263119,Carex_rostrata:1.263119)58.2/100:0.150987)100/100:4.343099)100/100:1.706131)100/100:2.056601,(Carex_arenaria:3.264108,Carex_divulsa:3.264108)100/100:6.255829)100/100:4.8575,Trichophorum_cespitosum:14.377436)47.5/100:0.397285,(Eriophorum_vaginatum:2.486033,Scirpus_sylvaticus:2.486033)100/100:12.288688)100/100:17.056208,((Cyperus_fuscus:13.585069,(Schoenoplectus_triqueter:0.099874,Schoenoplectus_lacustris:0.099874)100/100:13.485195)100/100:6.251639,Eleocharis_quinqueflora:19.836708)100/100:11.994221)100/100:28.524794,((Juncus_effusus:20.474768,Juncus_squarrosus:20.474768)100/100:30.892241,(Luzula_pallescens:2.7799,Luzula_sylvatica:2.7799)100/100:48.58711)100/100:8.988714)100/100:19.555977)100/100:3.393692,Sparganium_emersum:83.305393)100/100:4.448853,Iris_foetidissima:87.754246)99.5/100:1.447792,Narthecium_ossifragum:89.202038)100/100:6.951044)100/100:15.573983)100/100:6.595678,(Ginkgo_biloba:88.272071,((juniperus_communis:41.723254,taxus_baccata:41.723254)100/100:39.773839,pinus_sylvestris:81.497093)100/100:6.774978)100/100:16.859315)100/100:3.910877,(Selaginella_selaginoides:93.05969,(Huperzia_selago:42.306713,Lycopodium_clavatum:42.306713)100/100:50.752977)100/100:8.16082)100/100:1.423264,((((Adiantum_capillus_veneris:58.567082,(Pteridium_aquilinum:54.88203,((((Asplenium_ceterach:11.471632,Asplenium_scolopendrium:11.471632)100/100:3.42394,(Asplenium_adiantum_nigrum:14.471458,(Asplenium_marinum:13.627247,(Asplenium_trichomanes:10.319903,Asplenium_viride:10.319903)100/100:3.307343)100/100:0.844211)9.7/65:0.424114)100/100:27.284645,(((Cystopteris_fragilis:11.059654,Cystopteris_montana:11.059654)100/100:13.96177,Gymnocarpium_robertianum:25.021424)100/100:15.199846,(((Onoclea_sensibilis:30.096957,Struthiopteris_spicant:30.096957)100/100:4.426124,Woodsia_ilvensis:34.523082)100/100:1.934522,(Thelypteris_palustris:25.853381,Phegopteris_connectilis:25.853381)100/100:10.604223)100/100:3.763666)86/92:1.958947)100/100:2.284954,((((Dryopteris_borreri:0.082726,Dryopteris_filix_mas:0.082726)100/100:11.046637,Dryopteris_dilatata:11.129364)100/100:16.521631,(Polystichum_lonchitis:6.369691,Polystichum_setiferum:6.369691)100/100:21.281304)100/100:10.117249,Polypodium_vulgare:37.768244)100/100:6.696927)100/100:10.416859)99.8/100:3.685052)100/100:11.461801,(Azolla_filiculoides:58.999224,Pilularia_globulifera:58.999224)100/100:11.029659)100/100:11.654224,Vandenboschia_speciosa:81.683107)100/100:14.394134,(((Equisetum_sylvaticum:8.502157,(Equisetum_arvense:2.378261,Equisetum_fluviatile:2.378261)100/100:6.123897)100/100:4.634049,Equisetum_pratense:13.136206)99.2/100:23.863794,Equisetum_telmateia:37)100/100:59.07724)100/100:3.720005)100/100:8.359109,((((((((((((Antitrichia_curtipendula:12.682685,Climacium_dendroides:12.682685)100/100:2.577706,Rhytidiadelphus_loreus:15.260391)99.2/69:0.575963,((Cratoneuron_filicinum:13.840649,Thuidium_tamariscinum:13.840649)100/100:1.923997,(Calliergon_cordifolium:4.966922,Straminergon_stramineum:4.966922)100/100:10.797725)23.3/69:0.071708)96.1/98:0.300961,(Hyocomium_armoricum:15.444711,((Pseudoscleropodium_purum:6.425543,Rhynchostegium_megapolitanum:6.425543)100/100:5.620511,Rhynchostegiella_tenella:12.046053)100/100:3.398658)100/98:0.692604)100/100:0.283842,(((Heterocladium_heteropterum:11.836218,Neckera_pumila:11.836218)100/100:1.721594,Isothecium_myosuroides:13.557812)100/100:1.387717,Hypnum_cupressiforme:14.945529)100/100:1.475628)100/100:1.125399,(Orthothecium_rufescens:14.389996,Pseudotaxiphyllum_elegans:14.389996)55.8/85:3.15656)99.9/90:2.457589,Plagiothecium_denticulatum:20.004145)99.4/90:5.772654,Isopterygiella_pulchella:25.776799)100/100:11.337191,Ulota_crispa:37.11399)100/100:10.146432,Bryoerythrophyllum_caledonicum:47.260422)100/100:20.306921,(Polytrichastrum_sexangulare:10.587015,(Polytrichum_commune:4.690111,Polytrichum_formosum:4.690111)100/100:5.896905)100/100:56.980328)100/100:14.642959,((Sphagnum_contortum:2.113979,Sphagnum_tenellum:2.113979)81.5/98:0.902369,Sphagnum_girgensohnii:3.016348)100/100:79.193953)100/100:9.227835)100/100:28.994936,Lunularia_cruciata:62.443201)100/100:0,Herbertus_hutchinsiae:62.443201)Root; `37:T3355,nuclear_mito = `((((((((((Myriophyllum_alterniflorum:0.1036735345,Umbilicus_rupestris:0.1306843326)1/100:0.0209221795,(Ribes_rubrum:0.0526062736,Saxifraga_aizoides:0.1044484911)1/100:0.0229298558)1/100:0.0163192381,((((((((Acaena_ovalifolia:0.0316725818,(((Rosa_agrestis:0.0061704014,Rosa_spinosissima:0.0039598706)0.98/99.7:0.0024524785,(Rosa_canina:0.0116979478,Rosa_rugosa:0.004872724)1/96.3:0.0012901881)1/100:0.0086507061,((Comarum_palustre:0.0278555239,(Fragaria_moschata:0.0045369199,Fragaria_vesca:0.0008259303)1/100:0.0153109437)1/100:0.009006198,(Potentilla_anserina:0.0263510559,(Potentilla_indica:0.0156712197,Potentilla_sterilis:0.0073213962)1/100:0.0074712357)1/100:0.0066001599)1/100:0.0070637131)1/17:0.0017856362):0.007626304,(Geum_rivale:0.0065393494,Geum_urbanum:0.0062498708)1/100:0.0455302451)1/100:0.0052750647,(Rubus_caesius:0.0087365516,Rubus_idaeus:0.004721101)1/100:0.0132950087)1/35.5:0.0112418211,Filipendula_ulmaria:0.0557198418)1/100:0.0326232083,(((Crataegus_laevigata:0.0097147274,(Pyrus_communis:0.0125681431,((Malus_domestica:0.0027335493,Malus_sylvestris:0.0027882784)1/100:0.0025487844,Malus_x_robusta:0.005405998)1/100:0.0033012356)1/100:0.0027849149)1/100:0.031850871,Prunus_padus:0.0333862948)1/100:0.0171861891,Dryas_octopetala:0.0383467483)1/45.5:0.0059130579)1/100:0.0345012284,(Frangula_alnus:0.0636732319,((Humulus_lupulus:0.0597227992,(Parietaria_judaica:0.0838256473,(Urtica_dioica:0.0266674476,Urtica_urens:0.0272688875)1/100:0.0792178879)1/100:0.0320030912)1/100:0.0151036412,(Ulmus_glabra:0.0049639931,Ulmus_minor:0.0087411984)1/100:0.0600595019)1/100:0.0159033732)1/100:0.0108357141)1/100:0.0110713542,((((Astragalus_alpinus:0.0108085097,Astragalus_glycyphyllos:0.0154869329)1/100:0.0364482389,(((Lathyrus_linifolius:0.0163906541,Vicia_sativa:0.0196573539)1/100:0.0251940453,((Medicago_arabica:0.0079465839,Medicago_lupulina:0.0076967947)1/100:0.0238634755,(Trifolium_dubium:0.0255484131,((Trifolium_fragiferum:0.0102375987,(Trifolium_occidentale:0.0082144358,Trifolium_subterraneum:0.0238667493)1/83.7:0.003229104)1/95.6:0.0022077588,Trifolium_striatum:0.0130732754)1/100:0.011389909)1/100:0.008666013)1/99.7:0.0044683743)1/100:0.0075334167,Ononis_reclinata:0.0353369353)1/100:0.025991395)1/100:0.026961374,Laburnum_anagyroides:0.0502586908)1/100:0.0638929681,((((Alnus_glutinosa:0.0027115088,Alnus_incana:0.0132208527)1/100:0.0187048051,Corylus_avellana:0.0221749668)1/100:0.0325378081,Myrica_gale:0.0534655307)1/100:0.0076566263,(Fagus_sylvatica:0.0355751414,((Quercus_petraea:0.0085118474,Quercus_robur:0.0040642636)1/100:0.0046472326,(Quercus_ilex:0.0052245736,Quercus_cerris:0.0134341476)1/74.5:0.0013569606)1/100:0.0300946493)1/100:0.0185094695)1/100:0.0211591804)1/74.8:0.0054063675)1/100:0.0080156581,((((Erodium_maritimum:0.0177590306,Erodium_moschatum:0.0190451179)1/100:0.0225176977,(Geranium_rotundifolium:0.0249984379,Geranium_molle:0.0337027395)1/100:0.0303878447)1/100:0.0702489283,((Chamaenerion_angustifolium:0.0279354887,Epilobium_hirsutum:0.0279320515)1/100:0.1034642479,((((Arabidopsis_thaliana:0.0248914063,Lepidium_didymum:0.0263477348)1/94.5:0.0041979634,(Barbarea_vulgaris:0.0131642065,((Cardamine_flexuosa:0.0004478841,Cardamine_hirsuta:0.003604817)1/100:0.0163311051,Nasturtium_officinale:0.0181198605)1/99.6:0.0039309645)1/100:0.0099146203)0.99/100:0.0098173017,((Arabis_hirsuta:0.0146591601,(Draba_incana:0.0189451179,Draba_verna:0.0351510757)1/100:0.0116750202)1/100:0.0127555158,Brassica_nigra:0.0416486442)0.68/86:0.0041851785)1/100:0.007590541,Matthiola_sinuata:0.0312257846)1/100:0.1243651964)0.76/99.8:0.0148342173)1/100:0.0093265812,((Malva_neglecta:0.1073026091,(Acer_campestre:0.0402856984,Aesculus_hippocastanum:0.0323358155)1/100:0.0528931816)1/99.7:0.0077496455,(Euonymus_europaeus:0.0992037475,(((((Euphorbia_lathyris:0.0267580315,Euphorbia_peplus:0.0369512968)1/100:0.0197247049,Euphorbia_maculata:0.049183394)1/100:0.0301857295,Mercurialis_annua:0.0779757653)1/100:0.0170855954,(Hypericum_androsaemum:0.018926985,(Hypericum_hirsutum:0.0139251311,Hypericum_pulchrum:0.0098470547)1/100:0.0171086188)1/100:0.1044078309)1/65.9:0.0056578124,(((Populus_tremula:0.0190357885,Populus_nigra:0.0075656006)1/100:0.008781568,(Salix_cinerea:0.0073664106,(Salix_caprea:0.0071549182,Salix_repens:0.0049823525)1/100:0.0090540992)1/100:0.0190939369)0.75/100:0.0481699285,Viola_odorata:0.0821608958)1/100:0.0106551698)1/100:0.0163970283)0.77/95:0.0055564162)0.55/100:0.0065517175)0.92/53.1:0.004394489)1/100:0.0108803982)0.63/100:0.0040271036,(((((Agrostemma_githago:0.056342681,(Arenaria_serpyllifolia:0.0286278236,Moehringia_trinervia:0.0219753545)1/100:0.0294180799)1/100:0.0128573232,(Spergula_arvensis:0.0292606473,(Spergularia_bocconei:0.0053071483,Spergularia_marina:0.0041479147)1/100:0.0292507703)1/100:0.0225025225)1/100:0.0395325931,((Blitum_bonus_henricus:0.0348698069,Chenopodium_album:0.0341306049)1/100:0.0172417181,Salicornia_ramosissima:0.0680061633)1/100:0.0279411059)1/100:0.0450503436,(Tamarix_gallica:0.1025703586,(((Fallopia_convolvulus:0.0245167956,(Polygonum_aviculare:0.0082030963,Polygonum_maritimum:0.0095347005)1/100:0.0279262988)1/100:0.0179655059,Oxyria_digyna:0.0595752864)1/100:0.0190144536,Persicaria_maculosa:0.0537920664)1/100:0.0585332703)1/99.8:0.013366558)1/100:0.0422688924,(((((((((((Ajuga_chamaepitys:0.0473581597,((((Ballota_nigra:0.0222631316,(Lamium_amplexicaule:0.0140188979,Lamium_purpureum:0.0077512995)1/100:0.0192860089)0.99/100:0.0101497649,Melittis_melissophyllum:0.0226950564)1/79.6:0.0056910664,Galeopsis_tetrahit:0.0342787123)1/100:0.0333820871,(Scutellaria_galericulata:0.0057456862,Scutellaria_minor:0.0080133249)1/100:0.0392603931)0.56/96.7:0.0069156036)1/100:0.0086163012,Prunella_vulgaris:0.0781517701)1/100:0.0125043011,(((Euphrasia_confusa:0.0293744641,Rhinanthus_minor:0.022893934)1/100:0.0070835149,Melampyrum_sylvaticum:0.0361398505)1/100:0.0501060251,Verbena_officinalis:0.056044834)0.85/99.6:0.0077150413)1/99.4:0.0061744069,(Verbascum_nigrum:0.0073877036,Verbascum_thapsus:0.0070587542)1/100:0.0547391103)1/100:0.0072338284,((Callitriche_obtusangula:0.0926653321,(Veronica_serpyllifolia:0.0233157621,(Veronica_scutellata:0.0253581757,((Veronica_arvensis:0.0123016703,Veronica_verna:0.0160293789)1/100:0.0119677806,Veronica_triphyllos:0.0318595915)1/100:0.007410464)1/100:0.0111578676)0.87/100:0.0595027884)1/100:0.0157019123,((Linaria_vulgaris:0.0451523941,Misopates_orontium:0.0273076833)1/100:0.0100989444,Cymbalaria_muralis:0.0337329359)1/100:0.0228797275)1/100:0.0133302794)1/100:0.0241250774,(Ligustrum_vulgare:0.0178885142,Syringa_vulgaris:0.0146875202)1/100:0.0653241293)1/100:0.0236920945,((((Cruciata_laevipes:0.0344171131,(Galium_aparine:0.0140166907,Galium_uliginosum:0.0096258265)1/100:0.0116435607)1/99.9:0.0075743114,Sherardia_arvensis:0.0334901957)1/100:0.1054664853,Pentaglottis_sempervirens:0.1227964455)0.97/79.9:0.0137035686,((Calystegia_soldanella:0.0131052315,Convolvulus_arvensis:0.0077663709)1/100:0.0741632562,(Solanum_dulcamara:0.0119079979,Solanum_nigrum:0.0088862261)1/100:0.0742434688)1/100:0.0208998227)0.71/100:0.0084386336)1/100:0.0163697179,Ilex_aquifolium:0.0714388079)0.85/99.5:0.0057030985,(((Sambucus_nigra:0.0616171131,Succisa_pratensis:0.0851314342)1/100:0.012643044,(Torilis_japonica:0.0795458001,(Hedera_helix:0.0375313438,Hydrocotyle_vulgaris:0.0570126124)1/100:0.0124733686)1/100:0.0357345557)1/96.8:0.0058084497,((((Arctium_minus:0.012348675,Carduus_nutans:0.0231108738)1/100:0.0142388926,Carlina_vulgaris:0.033189443)1/100:0.0072069529,((((((Jacobaea_maritima:0.0053503597,Jacobaea_vulgaris:0.0077216275)1/100:0.015794205,Senecio_sylvaticus:0.0208961216)1/100:0.0086584883,(Petasites_albus:0.0091125889,(Petasites_hybridus:0.0109396863,Tussilago_farfara:0.0149602356)1/11.4:0.0042486198)1/100:0.0132109669)1/100:0.0263191152,((Calendula_officinalis:0.0463065825,(Tripolium_pannonicum:0.0162544399,Galatella_linosyris:0.0130139086)0.96/100:0.0269757361)1/95.7:0.0044325903,(((Filago_lutescens:0.0110858967,Logfia_minima:0.0092055109)1/100:0.0049641171,(Gnaphalium_uliginosum:0.0116536982,Pseudognaphalium_luteoalbum:0.0127637995)0.64/99.9:0.0026364766)1/100:0.022158159,((Matricaria_chamomilla:0.0070215782,Matricaria_discoidea:0.0075619804)1/100:0.0098844391,(Tanacetum_vulgare:0.0071433843,Tanacetum_parthenium:0.0144315848)1/99.5:0.0023913511)1/100:0.0439192659)1/44.5:0.004770583)0.91/100:0.0058118593)1/99.2:0.0061047813,Pulicaria_dysenterica:0.0385464693)1/100:0.0083013704,(Lapsana_communis:0.0489700778,Tragopogon_pratensis:0.0329309422)1/100:0.0156782316)1/99.8:0.0051182961)0.84/100:0.0601638506,(Jasione_montana:0.0635169317,(Lobelia_dortmanna:0.0242090523,Lobelia_urens:0.0127569671)1/100:0.0326459109)1/100:0.0275770494)1/100:0.0240363773)1/100:0.0123666373)1/100:0.0055481564,Cornus_suecica:0.0855200724)0.9/63.9:0.0042853035,(((Calluna_vulgaris:0.0435234173,Vaccinium_vitis_idaea:0.0325915714)1/100:0.0493392276,((Primula_veris:0.0037580855,Primula_vulgaris:0.0033073434)1/100:0.0789475487,Samolus_valerandi:0.0617470653)1/100:0.0406059531)1/99.7:0.010316622,(Impatiens_glandulifera:0.0248854288,Impatiens_parviflora:0.0142980611)1/100:0.1221906068)0.99/100:0.0139152055)1/100:0.0115205606)1/87.5:0.00500731)1/83:0.025172306,Buxus_sempervirens:0.0860669817)1/100:0.0087918853,(((Adonis_annua:0.0606043345,(Ranunculus_sardous:0.0261135225,Ranunculus_sceleratus:0.0195023057)1/100:0.0629060944)1/100:0.0127096628,(Aquilegia_vulgaris:0.0189382686,Thalictrum_minus:0.0184096205)1/100:0.0353028679)1/100:0.0367502013,Berberis_vulgaris:0.086041256)1/100:0.0254285091)1/99.4:0.0250998192,(((Aponogeton_distachyos:0.123709765,(Potamogeton_natans:0.0940984613,(Triglochin_maritima:0.0162881064,Triglochin_palustris:0.013847866)1/100:0.0898388592)1/100:0.0209462803)1/91.9:0.0347689422,Lemna_minuta:0.1858686671)0.99/99.9:0.0132659333,(((((((Bromus_sterilis:0.0403435227,(Poa_chaixii:0.0310973637,Polypogon_viridis:0.0194739177)1/100:0.0131502463)1/100:0.0432082887,Leersia_oryzoides:0.0468276275)0.98/100:0.0146637418,(Digitaria_sanguinalis:0.0438025649,Phragmites_australis:0.029997093)1/100:0.0169198483)1/100:0.1066146111,(((((Carex_depauperata:0.0108145312,(((((Carex_hirta:0.0041162312,Carex_riparia:0.0053236642)0.81/64.9:0.0006817449,Carex_rostrata:0.0040189566)1/100:0.002802626,Carex_nigra:0.0108594846)1/92.6:0.000602554,(Carex_caryophyllea:0.0077819927,Carex_acutiformis:0.0053815013)0.84/99.7:0.0015770095)0.34/99.2:0.0011412899,((Carex_extensa:0.0069963236,(Carex_distans:0.0047007828,Carex_laevigata:0.0060878146)1/99.9:0.0015077611)1/100:0.0021717297,(Carex_pendula:0.0031346681,Carex_sylvatica:0.0046152289)1/95.7:0.000579064)1/100:0.002540853)0.96/96.3:0.0018281901)1/100:0.0028300249,(Carex_arenaria:0.0082923727,Carex_divulsa:0.0072543223)1/100:0.0057303462)1/100:0.0123405529,((Eriophorum_vaginatum:0.0138784394,Scirpus_sylvaticus:0.00781236)1/100:0.0079202953,Trichophorum_cespitosum:0.016128415)1/99.7:0.0040565966)1/100:0.0193211325,((Cyperus_fuscus:0.0337976802,(Schoenoplectus_triqueter:0.0043020762,Schoenoplectus_lacustris:0.0047732325)1/100:0.0278529782)1/100:0.0087123099,Eleocharis_quinqueflora:0.0469998668)0.87/99.8:0.0052768437)1/100:0.0478905168,((Juncus_effusus:0.0367371863,Juncus_squarrosus:0.0599390586)1/100:0.0340929864,(Luzula_pallescens:0.0083570977,Luzula_sylvatica:0.0056872096)1/100:0.0686926534)1/100:0.0527651442)1/100:0.050137189)1/100:0.0288744483,Sparganium_emersum:0.0794758278)1/100:0.0231672135,Narthecium_ossifragum:0.1356874504)1/26.2:0.0075378297,Iris_foetidissima:0.1115480109)1/100:0.019912853)1/100:0.0256972665)1/100:0.256700998,(((((((Calliergon_cordifolium:0.006546612,Straminergon_stramineum:0.0110803598)1/100:0.0065128871,((Antitrichia_curtipendula:0.0254042546,(Climacium_dendroides:0.0175890876,Rhytidiadelphus_loreus:0.0175710202)11.5:0.0009810618)0.76/96.2:0.0011758219,((Cratoneuron_filicinum:0.0283509736,(Thuidium_tamariscinum:0.0169749593,Hypnum_cupressiforme:0.0189194246)1/100:0.0071826712)0.83/98.4:0.001592049,((Hyocomium_armoricum:0.0115092153,((Pseudoscleropodium_purum:0.006184379,Rhynchostegium_megapolitanum:0.0169104254)1/67.9:0.0020980344,Rhynchostegiella_tenella:0.0194634571)1/100:0.0025297148)1/100:0.0024073312,(Heterocladium_heteropterum:0.0218499152,Neckera_pumila:0.0146143484)0.81/100:0.0033644759)1/93.7:0.0010618761)1/65.4:0.0011807401)0.54/66.7:0.0010945075)0.51/98:0.0019999236,(Orthothecium_rufescens:0.0208572046,((Plagiothecium_denticulatum:0.0164348978,Pseudotaxiphyllum_elegans:0.0122632082)1/100:0.005640108,Isopterygiella_pulchella:0.0106924919)0.62/96.6:0.0011428395)0.86/85.7:0.0010667835)0.99/100:0.0240863371,Ulota_crispa:0.0506602287)1/100:0.0232018461,Bryoerythrophyllum_caledonicum:0.067207731)1/100:0.0603714581,(Polytrichastrum_sexangulare:0.0097975325,(Polytrichum_commune:0.0171465602,Polytrichum_formosum:0.011973801)1/100:0.0087522349)1/100:0.0691988475)1/100:0.0519917317,(Sphagnum_tenellum:0.0052496232,(Sphagnum_contortum:0.0073849901,Sphagnum_girgensohnii:0.0089878759)1/43:0.0021989511)0.99/100:0.1094168668)1/100:0.0655828661)1/100:0.0764077878,Lunularia_cruciata:0.1196796628)1/100:0,Herbertus_hutchinsiae:0.1554659938)Root; `38:T2d81,mito_nuclear = `(((((((((Myriophyllum_alterniflorum:46.742686,Umbilicus_rupestris:46.742686)99.8/100:5.127168,(Ribes_rubrum:28.126271,Saxifraga_aizoides:28.12627)100/100:23.743584)99.8/100:72.945247,((((((((((Acaena_ovalifolia:132.567471,(((Rosa_agrestis:0.107324,Rosa_canina:0.107324)98.3/100:0.670103,Rosa_spinosissima:0.777427)78.7/100:0.605239,Rosa_rugosa:1.382666)100/100:131.184805):0.288079,((Comarum_palustre:8.201362,(Fragaria_moschata:0.594634,Fragaria_vesca:0.594634)100/100:7.606728)100/100:18.892044,(Potentilla_anserina:13.529333,(Potentilla_indica:9.09961,Potentilla_sterilis:9.09961)99.2/100:4.429722)100/100:13.564074)100/100:105.185986)10.8/98:0.663946,(Rubus_caesius:4.966326,Rubus_idaeus:4.966326)100/100:126.649119)99.9/100:0.299208,(Geum_rivale:0.003397,Geum_urbanum:0.003397)100/100:131.312841)54.2/100:0.969928,Filipendula_ulmaria:130.346309)89.3/99:2.713717,((((Crataegus_laevigata:0.487985,Pyrus_communis:0.487985)35.8/100:0.094195,(Malus_domestica:0.153464,(Malus_sylvestris:0.001684,Malus_x_robusta:0.001684)0/100:0.151781)96.5/100:0.428715)100/100:10.428935,Prunus_padus:11.011115)100/100:7.66693,Dryas_octopetala:18.678045)79.5/100:108.954548)100/100:2.00906,(Frangula_alnus:56.459539,((Humulus_lupulus:44.855982,(Parietaria_judaica:39.043823,(Urtica_dioica:3.010487,Urtica_urens:3.010487)100/100:36.033336)99.6/100:5.812158)99.9/100:2.798265,(Ulmus_glabra:0.00208,Ulmus_minor:0.00208)100/100:47.652167)100/100:8.805292)100/100:69.163994)100/100:0.398336,((((Astragalus_alpinus:1.453175,Astragalus_glycyphyllos:1.453175)100/100:11.755881,((Lathyrus_linifolius:4.497537,Vicia_sativa:4.497537)100/100:2.543125,(((Medicago_arabica:1.641175,Medicago_lupulina:1.641175)100/100:4.459163,(Trifolium_dubium:4.855476,(((Trifolium_fragiferum:1.377587,Trifolium_occidentale:1.377587)97.2/100:1.019396,Trifolium_subterraneum:2.396983)88.6/100:0.307959,Trifolium_striatum:2.704942)100/100:2.150534)96.8/100:1.244862)85.6/99:0.320061,Ononis_reclinata:6.4204)91.8/99:0.620262)100/100:6.168394)100/100:7.805552,Laburnum_anagyroides:21.014609)100/100:45.694741,((((Alnus_glutinosa:0.060906,Alnus_incana:0.060906)99.9/100:3.153717,Corylus_avellana:3.214623)100/100:10.548469,Myrica_gale:13.763092)98/100:26.71957,(Fagus_sylvatica:37.8,((Quercus_petraea:0.132244,Quercus_robur:0.132244)99.7/100:3.263889,Quercus_ilex:3.396133)100/100:34.403867)100/100:2.682662)100/100:26.226687)1.4/32:58.515847)99.6/100:0.225197,((((Erodium_maritimum:3.666492,Erodium_moschatum:3.666492)99.2/100:4.841662,(Geranium_rotundifolium:3.288658,Geranium_molle:3.288658)100/100:5.219496)100/100:84.581882,(Chamaenerion_angustifolium:6.421446,Epilobium_hirsutum:6.421446)100/100:86.66859)98.8/100:7.051856,(((((((Arabidopsis_thaliana:4.616691,Lepidium_didymum:4.616691)80.1/100:0.561633,(Barbarea_vulgaris:2.93784,((Cardamine_flexuosa:0.043824,Cardamine_hirsuta:0.043824)100/100:2.652183,Nasturtium_officinale:2.696007)84/100:0.241833)100/100:2.240484)99.4/100:2.220465,((Arabis_hirsuta:3.357337,(Draba_incana:2.928572,Draba_verna:2.928572)95.9/100:0.428765)99.8/100:2.34543,Brassica_nigra:5.702767)95.8/100:1.696021)84.9/100:5.513388,Matthiola_sinuata:12.912177)100/100:47.526112,Malva_neglecta:60.438288)94.6/100:2.565426,(Acer_campestre:10.982836,Aesculus_hippocastanum:10.982836)100/100:52.020878)99.9/100:11.734869,(Euonymus_europaeus:73.843944,((((Euphorbia_lathyris:14.091356,Euphorbia_peplus:14.091356)96/100:3.303459,Euphorbia_maculata:17.394816)100/100:32.252637,Mercurialis_annua:49.647453)100/100:18.826744,(((Hypericum_androsaemum:3.220125,(Hypericum_hirsutum:1.232081,Hypericum_pulchrum:1.232081)100/100:1.988043)100/100:62.206134,(Populus_tremula:48.805882,(Populus_nigra:48.5,(Salix_caprea:1.860413,(Salix_cinerea:0.001841,Salix_repens:0.001841)0/100:1.858572)100/100:46.639587)94.2/100:0.305882)100/100:16.620377)63.6/100:2.091493,Viola_odorata:67.517752)94/99:0.956444)100/100:5.369748)15.7/71:0.894639)98.8/100:25.403309)61.1/75:24.858108)98.4/99:0.167491,((((((Agrostemma_githago:14.308749,(Arenaria_serpyllifolia:6.869318,Moehringia_trinervia:6.869318)100/100:7.439431)90.6/100:1.848982,(Spergula_arvensis:10.399378,(Spergularia_bocconei:0.051883,Spergularia_marina:0.051883)100/100:10.347495)100/100:5.758353)100/100:16.72766,((Blitum_bonus_henricus:7.925221,Chenopodium_album:7.925221)97.6/100:4.700352,Salicornia_ramosissima:12.625572)100/100:20.259819)100/100:37.319844,Tamarix_gallica:70.205236)47.7/98:14.775161,(((Fallopia_convolvulus:66,(Polygonum_aviculare:1.805023,Polygonum_maritimum:1.805023)100/100:64.194977)8.3/80:0.329666,Oxyria_digyna:66.329666)99.7/100:1.3533,Persicaria_maculosa:67.682966)100/100:17.297431)100/100:36.067572,(((((((((((Ajuga_chamaepitys:27.183752,((((Ballota_nigra:2.891649,(Lamium_amplexicaule:0.97501,Lamium_purpureum:0.97501)99.4/100:1.916639)63.9/78:0.862517,Melittis_melissophyllum:3.754166)66.1/78:1.57549,Galeopsis_tetrahit:5.329656)100/100:19.668968,(Scutellaria_galericulata:0.153163,Scutellaria_minor:0.153163)100/100:24.845462)94/100:2.185127)97.7/100:0.636248,Prunella_vulgaris:27.82)100/100:2.837992,((Euphrasia_confusa:5.575948,Rhinanthus_minor:5.575948)87.7/100:2.299295,Melampyrum_sylvaticum:7.875243)100/100:22.782749)99.1/100:0.925666,(Verbena_officinalis:15.120211,(Verbascum_nigrum:0.053499,Verbascum_thapsus:0.053499)100/100:15.066712)100/100:16.463447)99.8/100:1.55925,((Callitriche_obtusangula:29.70762,((Veronica_serpyllifolia:5.446113,Veronica_scutellata:5.446113)91.7/100:1.071835,((Veronica_arvensis:2.7782,Veronica_verna:2.7782)97.9/100:1.627799,Veronica_triphyllos:4.405999)99.4/100:2.111948)100/100:23.189672)99.9/100:2.100654,((Linaria_vulgaris:8.589782,Misopates_orontium:8.589782)99/100:3.176866,Cymbalaria_muralis:11.766648)99.7/100:20.041626)98.8/100:1.334634)100/100:6.1832,(Ligustrum_vulgare:2.75075,Syringa_vulgaris:2.75075)100/100:36.575359)100/100:13.190292,((Quercus_cerris:38.60298,((Cruciata_laevipes:1.760754,(Galium_aparine:1.124346,Galium_uliginosum:1.124346)96.7/100:0.636408)99.9/100:1.394333,Sherardia_arvensis:3.155087)100/100:35.447893)100/100:11.316074,Pentaglottis_sempervirens:49.919054)61.8/75:2.597347)49.7/74:2.368458,((Calystegia_soldanella:1.940441,Convolvulus_arvensis:1.940441)100/100:45.896215,(Solanum_dulcamara:33.9,Solanum_nigrum:33.9)100/100:13.936656)100/100:7.048203)100/100:9.336966,(Ilex_aquifolium:60.998765,((Sambucus_nigra:19.03286,Succisa_pratensis:19.03286)100/100:40.536853,((Torilis_japonica:53.311535,(Hedera_helix:21.509465,Hydrocotyle_vulgaris:21.509465)99.8/100:31.802071)100/100:5.62796,(((Arctium_minus:1.595348,Carduus_nutans:1.595348)100/100:46.179006,(Carlina_vulgaris:47.647875,(((((((Jacobaea_maritima:0.000611,Jacobaea_vulgaris:0.000611)99.1/100:1.022296,Senecio_sylvaticus:1.022907)91.8/99:0.50755,((Petasites_albus:0.274754,Petasites_hybridus:0.274754)60.2/100:0.081725,Tussilago_farfara:0.356479)91.2/100:1.173977)100/100:3.929565,Calendula_officinalis:5.460022)3.6/57:0.695487,((Tripolium_pannonicum:0.669932,Galatella_linosyris:0.669932)100/100:5.074378,((Filago_lutescens:0.320685,Logfia_minima:0.320685)99.5/100:1.609844,(Gnaphalium_uliginosum:1.602163,Pseudognaphalium_luteoalbum:1.602163)88.7/100:0.328366)100/100:3.813782)78.7/99:0.411199)83.5/98:3.366774,((((Matricaria_chamomilla:0.293511,Matricaria_discoidea:0.293511)99.8/100:0.65852,Tanacetum_vulgare:0.952031)99.8/100:1.265379,Tanacetum_parthenium:2.21741)100/100:6.491948,Pulicaria_dysenterica:8.709359)92.2/100:0.812925)86.9/100:37.937717,(Lapsana_communis:12.048601,Tragopogon_pratensis:12.048601)99.9/100:35.411399)95.5/100:0.187875)61.3/99:0.126479)100/100:7.507457,(Jasione_montana:26.002716,(Lobelia_dortmanna:7.943033,Lobelia_urens:7.943033)100/100:18.059683)100/100:29.279095)100/100:3.657685)62.4/96:0.630218)98/100:1.429052)86.9/99:3.22306)95.4/98:49.752368,(((Calluna_vulgaris:66,Vaccinium_vitis_idaea:66)100/100:45.001211,((Primula_veris:0.246904,Primula_vulgaris:0.246904)100/100:28.096421,Samolus_valerandi:28.343326)100/100:82.657886)39.8/37:0.66459,(Impatiens_glandulifera:0.687649,Impatiens_parviflora:0.687649)100/100:110.978152)100/100:2.308391)20.3/45:0.433102,Cornus_suecica:114.407295)100/100:6.640673)64.8/77:3.784541)99.8/91:0.017408)37.3/76:0.359493,Buxus_sempervirens:124.455608)100/100:0.265133,(((Adonis_annua:34.405434,(Ranunculus_sardous:4.634709,Ranunculus_sceleratus:4.634709)100/100:29.770725)99.9/100:21.594566,(Aquilegia_vulgaris:14.326715,Thalictrum_minus:14.326715)100/100:41.673285)100/100:9.562751,Berberis_vulgaris:65.562751)100/100:58.627725)100/100:0.191776,(((Aponogeton_distachyos:43.141987,(Potamogeton_natans:29.952021,(Triglochin_maritima:1.319346,Triglochin_palustris:1.319346)100/100:28.632675)100/100:13.189966)100/100:61.715154,Lemna_minuta:104.857141)97.8/100:8.142859,(((((((Bromus_sterilis:10.87137,(Poa_chaixii:7.223609,Polypogon_viridis:7.223609)99.8/100:3.64776)100/100:18.262838,Leersia_oryzoides:29.134207)17.1/100:1.305793,(Digitaria_sanguinalis:10.916558,Phragmites_australis:10.916558)99.2/100:19.523442)100/100:44.280313,(((((((Carex_hirta:0.68274,Carex_riparia:0.68274)83.8/96:0.543448,Carex_rostrata:1.226188)99.4/100:2.894136,(((Carex_depauperata:3.36326,Carex_caryophyllea:3.36326)75.5/99:0.08509,(Carex_nigra:1.210612,Carex_acutiformis:1.210612)97.2/100:2.237738)93.8/100:0.572049,(((Carex_extensa:2.645698,Carex_distans:2.645698)61/100:0.294382,Carex_laevigata:2.94008)100/100:0.900661,(Carex_pendula:2.871951,Carex_sylvatica:2.871951)96.5/100:0.96879)88.8/99:0.179658)41.9/98:0.099925)100/100:4.315327,(Carex_arenaria:2.106747,Carex_divulsa:2.106747)100/100:6.328904)100/100:9.609864,((Eriophorum_vaginatum:6.488387,Scirpus_sylvaticus:6.488387)100/100:8.405196,Trichophorum_cespitosum:14.893583)50.9/98:3.151932)100/100:13.438233,((Cyperus_fuscus:20.74179,(Schoenoplectus_triqueter:1.386569,Schoenoplectus_lacustris:1.386569)100/100:19.355221)100/100:7.532122,Eleocharis_quinqueflora:28.273912)99.9/100:3.209836)100/100:22.218485,((Juncus_effusus:8.143771,Juncus_squarrosus:8.143771)100/100:7.694315,(Luzula_pallescens:1.056958,Luzula_sylvatica:1.056958)100/100:14.781128)100/100:37.864147)100/100:21.01808)99.7/100:3.845595,Sparganium_emersum:78.565908)100/100:7.732204,Narthecium_ossifragum:86.298112)17.2/89:1.777351,Iris_foetidissima:88.075462)100/100:24.924538)100/100:10.9987)97.8/100:54.733876,((((((((((Antitrichia_curtipendula:2.447692,Climacium_dendroides:2.447692)97.1/100:1.826342,(Cratoneuron_filicinum:3.358389,Thuidium_tamariscinum:3.358389)89.5/100:0.915644)0/96:0.001477,Rhytidiadelphus_loreus:4.27551)60.7/97:0.481593,(((Calliergon_cordifolium:0.707883,Straminergon_stramineum:0.707883)99.4/100:3.20307,(Hyocomium_armoricum:3.363665,((Pseudoscleropodium_purum:0.812044,Rhynchostegium_megapolitanum:0.812044)91/100:1.186123,Rhynchostegiella_tenella:1.998168)100/100:1.365497)90.2/99:0.547288)79/100:0.544168,(Hypnum_cupressiforme:4.205286,(Heterocladium_heteropterum:2.859549,Neckera_pumila:2.859549)91.4/100:1.345737)86.5/58:0.249835)86.7/58:0.301982)95.4/100:0.729419,((Orthothecium_rufescens:4.199263,Plagiothecium_denticulatum:4.199263)92.3/100:0.923685,Pseudotaxiphyllum_elegans:5.122948)86.8/84:0.363574)78.2/100:0.672876,Isopterygiella_pulchella:6.159398)100/100:9.81889,Ulota_crispa:15.978288)100/100:7.481866,Bryoerythrophyllum_caledonicum:23.460154)100/100:10.35984,(Polytrichastrum_sexangulare:2.650781,(Polytrichum_commune:1.884972,Polytrichum_formosum:1.884972)94.5/100:0.765808)100/100:31.169213)100/100:12.376562,((Sphagnum_tenellum:1.37586,Sphagnum_contortum:1.37586)91.4/100:0.468597,Sphagnum_girgensohnii:1.844457)100/100:44.352098)100/100:23.068268)100/100:49.658814,Lunularia_cruciata:19.60601)100/100:0,Herbertus_hutchinsiae:19.60601)Root; `39:T3358,plastid_nuclear = `((((((((((((((((Acaena_ovalifolia:0.0316725818,(((Comarum_palustre:0.0278555239,(Fragaria_moschata:0.0045369199,Fragaria_vesca:0.0008259303)1/100:0.0153109437)1/100:0.009006198,(Potentilla_anserina:0.0263510559,(Potentilla_indica:0.0156712197,Potentilla_sterilis:0.0073213962)1/100:0.0074712357)1/100:0.0066001599)1/100:0.0070637131,((Rosa_canina:0.0116979478,Rosa_rugosa:0.004872724)1/96.3:0.0012901881,(Rosa_agrestis:0.0061704014,Rosa_spinosissima:0.0039598706)0.98/99.7:0.0024524785)1/100:0.0086507061)1/17:0.0017856362):0.007626304,(Geum_rivale:0.0065393494,Geum_urbanum:0.0062498708)1/100:0.0455302451)1/100:0.0052750647,(Rubus_caesius:0.0087365516,Rubus_idaeus:0.004721101)1/100:0.0132950087)1/35.5:0.0112418211,Filipendula_ulmaria:0.0557198418)1/100:0.0326232083,(Dryas_octopetala:0.0383467483,((Crataegus_laevigata:0.0097147274,((Malus_x_robusta:0.005405998,(Malus_domestica:0.0027335493,Malus_sylvestris:0.0027882784)1/100:0.0025487844)1/100:0.0033012356,Pyrus_communis:0.0125681431)1/100:0.0027849149)1/100:0.031850871,Prunus_padus:0.0333862948)1/100:0.0171861891)1/45.5:0.0059130579)1/100:0.0345012284,(Frangula_alnus:0.0636732319,((Humulus_lupulus:0.0597227992,(Parietaria_judaica:0.0838256473,(Urtica_dioica:0.0266674476,Urtica_urens:0.0272688875)1/100:0.0792178879)1/100:0.0320030912)1/100:0.0151036412,(Ulmus_glabra:0.0049639931,Ulmus_minor:0.0087411984)1/100:0.0600595019)1/100:0.0159033732)1/100:0.0108357141)1/100:0.0110713542,(((((Alnus_glutinosa:0.0027115088,Alnus_incana:0.0132208527)1/100:0.0187048051,Corylus_avellana:0.0221749668)1/100:0.0325378081,Myrica_gale:0.0534655307)1/100:0.0076566263,(Fagus_sylvatica:0.0355751414,((Quercus_ilex:0.0052245736,Quercus_cerris:0.0134341476)1/74.5:0.0013569606,(Quercus_petraea:0.0085118474,Quercus_robur:0.0040642636)1/100:0.0046472326)1/100:0.0300946493)1/100:0.0185094695)1/100:0.0211591804,(((Astragalus_alpinus:0.0108085097,Astragalus_glycyphyllos:0.0154869329)1/100:0.0364482389,(((Lathyrus_linifolius:0.0163906541,Vicia_sativa:0.0196573539)1/100:0.0251940453,((Trifolium_dubium:0.0255484131,((Trifolium_fragiferum:0.0102375987,(Trifolium_occidentale:0.0082144358,Trifolium_subterraneum:0.0238667493)1/83.7:0.003229104)1/95.6:0.0022077588,Trifolium_striatum:0.0130732754)1/100:0.011389909)1/100:0.008666013,(Medicago_arabica:0.0079465839,Medicago_lupulina:0.0076967947)1/100:0.0238634755)1/99.7:0.0044683743)1/100:0.0075334167,Ononis_reclinata:0.0353369353)1/100:0.025991395)1/100:0.026961374,Laburnum_anagyroides:0.0502586908)1/100:0.0638929681)1/74.8:0.0054063675)1/100:0.0080156581,(((Euonymus_europaeus:0.0992037475,(((Hypericum_androsaemum:0.018926985,(Hypericum_hirsutum:0.0139251311,Hypericum_pulchrum:0.0098470547)1/100:0.0171086188)1/100:0.1044078309,(((Euphorbia_lathyris:0.0267580315,Euphorbia_peplus:0.0369512968)1/100:0.0197247049,Euphorbia_maculata:0.049183394)1/100:0.0301857295,Mercurialis_annua:0.0779757653)1/100:0.0170855954)1/65.9:0.0056578124,(((Populus_nigra:0.0075656006,Populus_tremula:0.0190357885)1/100:0.008781568,((Salix_caprea:0.0071549182,Salix_repens:0.0049823525)1/100:0.0090540992,Salix_cinerea:0.0073664106)1/100:0.0190939369)0.75/100:0.0481699285,Viola_odorata:0.0821608958)1/100:0.0106551698)1/100:0.0163970283)0.77/95:0.0055564162,((Acer_campestre:0.0402856984,Aesculus_hippocastanum:0.0323358155)1/100:0.0528931816,Malva_neglecta:0.1073026091)1/99.7:0.0077496455)0.55/100:0.0065517175,((((((Arabidopsis_thaliana:0.0248914063,Lepidium_didymum:0.0263477348)1/94.5:0.0041979634,(Barbarea_vulgaris:0.0131642065,((Cardamine_flexuosa:0.0004478841,Cardamine_hirsuta:0.003604817)1/100:0.0163311051,Nasturtium_officinale:0.0181198605)1/99.6:0.0039309645)1/100:0.0099146203)0.99/100:0.0098173017,((Arabis_hirsuta:0.0146591601,(Draba_incana:0.0189451179,Draba_verna:0.0351510757)1/100:0.0116750202)1/100:0.0127555158,Brassica_nigra:0.0416486442)0.68/86:0.0041851785)1/100:0.007590541,Matthiola_sinuata:0.0312257846)1/100:0.1243651964,(Chamaenerion_angustifolium:0.0279354887,Epilobium_hirsutum:0.0279320515)1/100:0.1034642479)0.76/99.8:0.0148342173,((Geranium_molle:0.0337027395,Geranium_rotundifolium:0.0249984379)1/100:0.0303878447,(Erodium_maritimum:0.0177590306,Erodium_moschatum:0.0190451179)1/100:0.0225176977)1/100:0.0702489283)1/100:0.0093265812)0.92/53.1:0.004394489)1/100:0.0108803982,((Myriophyllum_alterniflorum:0.1036735345,Umbilicus_rupestris:0.1306843326)1/100:0.0209221795,(Ribes_rubrum:0.0526062736,Saxifraga_aizoides:0.1044484911)1/100:0.0229298558)1/100:0.0163192381)0.63/100:0.0040271036,(((((Agrostemma_githago:0.056342681,(Arenaria_serpyllifolia:0.0286278236,Moehringia_trinervia:0.0219753545)1/100:0.0294180799)1/100:0.0128573232,(Spergula_arvensis:0.0292606473,(Spergularia_bocconei:0.0053071483,Spergularia_marina:0.0041479147)1/100:0.0292507703)1/100:0.0225025225)1/100:0.0395325931,((Blitum_bonus_henricus:0.0348698069,Chenopodium_album:0.0341306049)1/100:0.0172417181,Salicornia_ramosissima:0.0680061633)1/100:0.0279411059)1/100:0.0450503436,((((Fallopia_convolvulus:0.0245167956,(Polygonum_aviculare:0.0082030963,Polygonum_maritimum:0.0095347005)1/100:0.0279262988)1/100:0.0179655059,Oxyria_digyna:0.0595752864)1/100:0.0190144536,Persicaria_maculosa:0.0537920664)1/100:0.0585332703,Tamarix_gallica:0.1025703586)1/99.8:0.013366558)1/100:0.0422688924,(((((((((((Ajuga_chamaepitys:0.0473581597,((((Ballota_nigra:0.0222631316,(Lamium_amplexicaule:0.0140188979,Lamium_purpureum:0.0077512995)1/100:0.0192860089)0.99/100:0.0101497649,Melittis_melissophyllum:0.0226950564)1/79.6:0.0056910664,Galeopsis_tetrahit:0.0342787123)1/100:0.0333820871,(Scutellaria_galericulata:0.0057456862,Scutellaria_minor:0.0080133249)1/100:0.0392603931)0.56/96.7:0.0069156036)1/100:0.0086163012,Prunella_vulgaris:0.0781517701)1/100:0.0125043011,(((Euphrasia_confusa:0.0293744641,Rhinanthus_minor:0.022893934)1/100:0.0070835149,Melampyrum_sylvaticum:0.0361398505)1/100:0.0501060251,Verbena_officinalis:0.056044834)0.85/99.6:0.0077150413)1/99.4:0.0061744069,(Verbascum_nigrum:0.0073877036,Verbascum_thapsus:0.0070587542)1/100:0.0547391103)1/100:0.0072338284,((Callitriche_obtusangula:0.0926653321,(Veronica_serpyllifolia:0.0233157621,(((Veronica_arvensis:0.0123016703,Veronica_verna:0.0160293789)1/100:0.0119677806,Veronica_triphyllos:0.0318595915)1/100:0.007410464,Veronica_scutellata:0.0253581757)1/100:0.0111578676)0.87/100:0.0595027884)1/100:0.0157019123,(Cymbalaria_muralis:0.0337329359,(Linaria_vulgaris:0.0451523941,Misopates_orontium:0.0273076833)1/100:0.0100989444)1/100:0.0228797275)1/100:0.0133302794)1/100:0.0241250774,(Ligustrum_vulgare:0.0178885142,Syringa_vulgaris:0.0146875202)1/100:0.0653241293)1/100:0.0236920945,(((Calystegia_soldanella:0.0131052315,Convolvulus_arvensis:0.0077663709)1/100:0.0741632562,(Solanum_dulcamara:0.0119079979,Solanum_nigrum:0.0088862261)1/100:0.0742434688)1/100:0.0208998227,((Sherardia_arvensis:0.0334901957,(Cruciata_laevipes:0.0344171131,(Galium_aparine:0.0140166907,Galium_uliginosum:0.0096258265)1/100:0.0116435607)1/99.9:0.0075743114)1/100:0.1054664853,Pentaglottis_sempervirens:0.1227964455)0.97/79.9:0.0137035686)0.71/100:0.0084386336)1/100:0.0163697179,Ilex_aquifolium:0.0714388079)0.85/99.5:0.0057030985,(((Sambucus_nigra:0.0616171131,Succisa_pratensis:0.0851314342)1/100:0.012643044,((Hedera_helix:0.0375313438,Hydrocotyle_vulgaris:0.0570126124)1/100:0.0124733686,Torilis_japonica:0.0795458001)1/100:0.0357345557)1/96.8:0.0058084497,(((((((((Tanacetum_parthenium:0.0144315848,Tanacetum_vulgare:0.0071433843)1/99.5:0.0023913511,(Matricaria_chamomilla:0.0070215782,Matricaria_discoidea:0.0075619804)1/100:0.0098844391)1/100:0.0439192659,((Filago_lutescens:0.0110858967,Logfia_minima:0.0092055109)1/100:0.0049641171,(Pseudognaphalium_luteoalbum:0.0127637995,Gnaphalium_uliginosum:0.0116536982)0.64/99.9:0.0026364766)1/100:0.022158159)1/44.5:0.004770583,((Galatella_linosyris:0.0130139086,Tripolium_pannonicum:0.0162544399)0.96/100:0.0269757361,Calendula_officinalis:0.0463065825)1/95.7:0.0044325903)0.91/100:0.0058118593,(((Jacobaea_maritima:0.0053503597,Jacobaea_vulgaris:0.0077216275)1/100:0.015794205,Senecio_sylvaticus:0.0208961216)1/100:0.0086584883,(Petasites_albus:0.0091125889,(Petasites_hybridus:0.0109396863,Tussilago_farfara:0.0149602356)1/11.4:0.0042486198)1/100:0.0132109669)1/100:0.0263191152)1/99.2:0.0061047813,Pulicaria_dysenterica:0.0385464693)1/100:0.0083013704,(Lapsana_communis:0.0489700778,Tragopogon_pratensis:0.0329309422)1/100:0.0156782316)1/99.8:0.0051182961,(Carlina_vulgaris:0.033189443,(Carduus_nutans:0.0231108738,Arctium_minus:0.012348675)1/100:0.0142388926)1/100:0.0072069529)0.84/100:0.0601638506,(Jasione_montana:0.0635169317,(Lobelia_dortmanna:0.0242090523,Lobelia_urens:0.0127569671)1/100:0.0326459109)1/100:0.0275770494)1/100:0.0240363773)1/100:0.0123666373)1/100:0.0055481564,Cornus_suecica:0.0855200724)0.9/63.9:0.0042853035,(((Calluna_vulgaris:0.0435234173,Vaccinium_vitis_idaea:0.0325915714)1/100:0.0493392276,((Primula_veris:0.0037580855,Primula_vulgaris:0.0033073434)1/100:0.0789475487,Samolus_valerandi:0.0617470653)1/100:0.0406059531)1/99.7:0.010316622,(Impatiens_glandulifera:0.0248854288,Impatiens_parviflora:0.0142980611)1/100:0.1221906068)0.99/100:0.0139152055)1/100:0.0115205606)1/87.5:0.00500731)1/83:0.025172306,Buxus_sempervirens:0.0860669817)1/100:0.0087918853,(((Aquilegia_vulgaris:0.0189382686,Thalictrum_minus:0.0184096205)1/100:0.0353028679,(Adonis_annua:0.0606043345,(Ranunculus_sardous:0.0261135225,Ranunculus_sceleratus:0.0195023057)1/100:0.0629060944)1/100:0.0127096628)1/100:0.0367502013,Berberis_vulgaris:0.086041256)1/100:0.0254285091)1/99.4:0.0250998192,((Lemna_minuta:0.1858686671,(Aponogeton_distachyos:0.123709765,(Potamogeton_natans:0.0940984613,(Triglochin_maritima:0.0162881064,Triglochin_palustris:0.013847866)1/100:0.0898388592)1/100:0.0209462803)1/91.9:0.0347689422)0.99/99.9:0.0132659333,((((((((((((Carex_sylvatica:0.0046152289,Carex_pendula:0.0031346681)1/95.7:0.000579064,((Carex_laevigata:0.0060878146,Carex_distans:0.0047007828)1/99.9:0.0015077611,Carex_extensa:0.0069963236)1/100:0.0021717297)1/100:0.002540853,((Carex_acutiformis:0.0053815013,Carex_caryophyllea:0.0077819927)0.84/99.7:0.0015770095,(Carex_nigra:0.0108594846,((Carex_hirta:0.0041162312,Carex_riparia:0.0053236642)0.81/64.9:0.0006817449,Carex_rostrata:0.0040189566)1/100:0.002802626)1/92.6:0.000602554)0.34/99.2:0.0011412899)0.96/96.3:0.0018281901,Carex_depauperata:0.0108145312)1/100:0.0028300249,(Carex_arenaria:0.0082923727,Carex_divulsa:0.0072543223)1/100:0.0057303462)1/100:0.0123405529,(Trichophorum_cespitosum:0.016128415,(Eriophorum_vaginatum:0.0138784394,Scirpus_sylvaticus:0.00781236)1/100:0.0079202953)1/99.7:0.0040565966)1/100:0.0193211325,((Cyperus_fuscus:0.0337976802,(Schoenoplectus_lacustris:0.0047732325,Schoenoplectus_triqueter:0.0043020762)1/100:0.0278529782)1/100:0.0087123099,Eleocharis_quinqueflora:0.0469998668)0.87/99.8:0.0052768437)1/100:0.0478905168,((Juncus_effusus:0.0367371863,Juncus_squarrosus:0.0599390586)1/100:0.0340929864,(Luzula_pallescens:0.0083570977,Luzula_sylvatica:0.0056872096)1/100:0.0686926534)1/100:0.0527651442)1/100:0.050137189,((Leersia_oryzoides:0.0468276275,(Bromus_sterilis:0.0403435227,(Poa_chaixii:0.0310973637,Polypogon_viridis:0.0194739177)1/100:0.0131502463)1/100:0.0432082887)0.98/100:0.0146637418,(Digitaria_sanguinalis:0.0438025649,Phragmites_australis:0.029997093)1/100:0.0169198483)1/100:0.1066146111)1/100:0.0288744483,Sparganium_emersum:0.0794758278)1/100:0.0231672135,Narthecium_ossifragum:0.1356874504)1/26.2:0.0075378297,Iris_foetidissima:0.1115480109)1/100:0.019912853)1/100:0.0256972665)1/100:0.256700998,(((((((Calliergon_cordifolium:0.006546612,Straminergon_stramineum:0.0110803598)1/100:0.0065128871,((Antitrichia_curtipendula:0.0254042546,(Climacium_dendroides:0.0175890876,Rhytidiadelphus_loreus:0.0175710202)11.5:0.0009810618)0.76/96.2:0.0011758219,((Cratoneuron_filicinum:0.0283509736,(Thuidium_tamariscinum:0.0169749593,Hypnum_cupressiforme:0.0189194246)1/100:0.0071826712)0.83/98.4:0.001592049,((Hyocomium_armoricum:0.0115092153,((Pseudoscleropodium_purum:0.006184379,Rhynchostegium_megapolitanum:0.0169104254)1/67.9:0.0020980344,Rhynchostegiella_tenella:0.0194634571)1/100:0.0025297148)1/100:0.0024073312,(Heterocladium_heteropterum:0.0218499152,Neckera_pumila:0.0146143484)0.81/100:0.0033644759)1/93.7:0.0010618761)1/65.4:0.0011807401)0.54/66.7:0.0010945075)0.51/98:0.0019999236,(Orthothecium_rufescens:0.0208572046,((Pseudotaxiphyllum_elegans:0.0122632082,Plagiothecium_denticulatum:0.0164348978)1/100:0.005640108,Isopterygiella_pulchella:0.0106924919)0.62/96.6:0.0011428395)0.86/85.7:0.0010667835)0.99/100:0.0240863371,Ulota_crispa:0.0506602287)1/100:0.0232018461,Bryoerythrophyllum_caledonicum:0.067207731)1/100:0.0603714581,(Polytrichastrum_sexangulare:0.0097975325,(Polytrichum_commune:0.0171465602,Polytrichum_formosum:0.011973801)1/100:0.0087522349)1/100:0.0691988475)1/100:0.0519917317,(Sphagnum_tenellum:0.0052496232,(Sphagnum_contortum:0.0073849901,Sphagnum_girgensohnii:0.0089878759)1/43:0.0021989511)0.99/100:0.1094168668)1/100:0.0655828661)1/100:0.0764077878,Lunularia_cruciata:0.1196796628)1/100:0,Herbertus_hutchinsiae:0.1554659938)Root; `3a:T2da0,nuclear_plastid = `(((((((((((((((((((Acaena_ovalifolia:133.646108,(((Comarum_palustre:6.291973,(Fragaria_moschata:0.088978,Fragaria_vesca:0.088978)100/100:6.202995)100/100:7.00356,(Potentilla_anserina:10.150512,(Potentilla_indica:5.024997,Potentilla_sterilis:5.024997)100/100:5.125515)100/100:3.145021)100/100:3.963129,((Rosa_canina:0.534566,Rosa_agrestis:0.534566)100/100:1.69734,(Rosa_rugosa:1.023443,Rosa_spinosissima:1.023443)100/100:1.208462)100/100:15.026756)28/93:116.387446):1.467999,(Rubus_caesius:5.435343,Rubus_idaeus:5.435343)100/100:126.742765)100/100:0.223865,(Geum_rivale:0.033339,Geum_urbanum:0.033339)100/100:131.920905)92.9/99:1.252374,Filipendula_ulmaria:130.701869)100/100:1.893402,Dryas_octopetala:128.808466)100/100:0.136241,((Crataegus_laevigata:1.539809,(((Malus_x_robusta:0.031691,Malus_domestica:0.031691)100/100:0.150819,Malus_sylvestris:0.18251)100/100:1.172281,Pyrus_communis:1.354791)75.4/100:0.185018)100/100:18.561784,Prunus_padus:20.101594)100/100:108.570632)97/99:1.737629,(Frangula_alnus:60.70695,((Humulus_lupulus:43.586852,(Parietaria_judaica:35.469835,(Urtica_dioica:9.972251,Urtica_urens:9.972251)100/100:25.497584)100/100:8.117017)100/100:8.867477,(Ulmus_glabra:0.016665,Ulmus_minor:0.016665)100/100:52.437664)100/100:8.25262)100/100:66.227647)100/100:1.012366,((((Alnus_glutinosa:0.080417,Alnus_incana:0.080417)100/100:8.949685,Corylus_avellana:9.030101)100/100:12.695531,Myrica_gale:21.725632)100/100:24.338055,(Fagus_sylvatica:37.8,(Quercus_ilex:1.964928,(Quercus_cerris:1.738437,(Quercus_petraea:0.008552,(Quercus_robur:0.00053,Tanacetum_parthenium:0.00053)75.6/100:0.008022)100/100:1.729885)95.6/100:0.226491)100/100:35.835072)100/100:8.263688)100/100:79.858543)100/100:0.127764,(((Astragalus_alpinus:6.719205,Astragalus_glycyphyllos:6.719205)100/100:30.541637,(((Lathyrus_linifolius:18.848132,Vicia_sativa:18.848132)100/100:9.985798,(Trifolium_dubium:21.661576,((Trifolium_fragiferum:7.908704,Trifolium_occidentale:7.908704)100/100:3.778072,(Trifolium_subterraneum:9.100318,Trifolium_striatum:9.100318)100/100:2.586458)100/100:9.9748)100/100:7.172355)100/100:0.784244,((Medicago_arabica:13.268892,Medicago_lupulina:13.268892)100/100:14.462167,Ononis_reclinata:27.731059)99.8/100:1.887116)100/100:7.642668)100/100:18.739158,Laburnum_anagyroides:56)100/100:69.794467)98.6/99:0.495065,(Euonymus_europaeus:107.154692,((Hypericum_androsaemum:13.29281,(Hypericum_hirsutum:6.860674,Hypericum_pulchrum:6.860674)100/100:6.432136)100/100:72.780484,((((Euphorbia_lathyris:12.383339,Euphorbia_peplus:12.383339)100/100:5.265442,Euphorbia_maculata:17.648782)100/100:26.421876,Mercurialis_annua:44.070658)100/100:33.759137,(((Populus_nigra:1.034544,Populus_tremula:1.034544)100/100:47.465456,((Salix_caprea:0.078338,Salix_repens:0.078337)79.8/99:0.03968,Salix_cinerea:0.118017)100/100:48.381983)100/100:21.432492,Viola_odorata:69.932492)100/100:7.897302)24/97:8.2435)100/100:21.081397)100/100:18.14471)100/100:0.299402,(((Acer_campestre:14.586313,Aesculus_hippocastanum:14.586313)100/100:63.326033,(Malva_neglecta:71.644575,((((Arabidopsis_thaliana:10.45902,Lepidium_didymum:10.45902)47.3/100:0.462266,(Barbarea_vulgaris:8.648753,((Cardamine_flexuosa:0.193731,Cardamine_hirsuta:0.193731)100/100:6.494676,Nasturtium_officinale:6.688408)100/100:1.960345)100/100:2.272534)100/100:3.040794,((Arabis_hirsuta:9.158835,(Draba_incana:6.378267,Draba_verna:6.378267)100/100:2.780568)100/100:3.713735,Brassica_nigra:12.87257)100/100:1.08951)66.7/100:0.749933,Matthiola_sinuata:14.712014)100/100:56.932561)100/100:6.26777)100/100:31.837893,((Chamaenerion_angustifolium:9.616184,Epilobium_hirsutum:9.616184)100/100:94.447494,((Geranium_molle:13.702964,Geranium_rotundifolium:13.702964)100/100:14.707782,(Erodium_maritimum:5.984251,Erodium_moschatum:5.984251)100/100:22.426495)100/100:75.652933)100/100:5.68656)100/100:15.249762)100/100:10.779723,((Myriophyllum_alterniflorum:61.363517,Umbilicus_rupestris:61.363517)100/100:10.258805,(Ribes_rubrum:46.89391,Saxifraga_aizoides:46.89391)100/100:24.728412)100/100:42.597955)100/100:1.220277,(((((Agrostemma_githago:28.290144,(Arenaria_serpyllifolia:13.178734,Moehringia_trinervia:13.178734)100/100:15.111409)100/100:2.172375,(Spergula_arvensis:20.211652,(Spergularia_bocconei:0.105461,Spergularia_marina:0.105461)100/100:20.106191)100/100:10.250867)100/100:23.278422,((Blitum_bonus_henricus:21.793091,Chenopodium_album:21.793091)100/100:11.991963,Salicornia_ramosissima:33.785054)100/100:19.955887)100/100:39.354881,((((Fallopia_convolvulus:66,(Polygonum_aviculare:0.97901,Polygonum_maritimum:0.97901)100/100:65.02099)100/100:2.001592,Oxyria_digyna:68.001592)100/100:1.67231,Persicaria_maculosa:69.673902)100/100:20.710301,Tamarix_gallica:90.384203)100/100:2.711619)100/100:15.344242,(((((((((((Ajuga_chamaepitys:25.004157,(((Ballota_nigra:7.804722,(Lamium_amplexicaule:3.755921,Lamium_purpureum:3.755921)100/100:4.048801)100/100:2.601233,(Melittis_melissophyllum:9.244408,Galeopsis_tetrahit:9.244408)100/100:1.161547)100/100:10.713997,(Scutellaria_galericulata:0.786469,Scutellaria_minor:0.786469)100/100:20.333482)100/100:3.884206)100/100:2.815843,(Prunella_vulgaris:22.140141,Matricaria_chamomilla:22.14014)100/100:5.67986)100/100:6.261458,((Euphrasia_confusa:16.881987,Rhinanthus_minor:16.881987)100/100:1.944142,Melampyrum_sylvaticum:18.826129)100/100:15.255329)99.6/100:0.61099,Verbena_officinalis:34.692448)100/100:0.732863,(Verbascum_nigrum:0.400608,Verbascum_thapsus:0.400608)100/100:35.024703)100/100:1.036221,((Callitriche_obtusangula:29.907273,((Veronica_serpyllifolia:14.13071,((Veronica_arvensis:7.248243,Veronica_verna:7.248243)100/100:5.236178,Veronica_triphyllos:12.48442)100/100:1.646289)95.8/100:0.475542,Veronica_scutellata:14.606252)100/100:15.301021)100/100:2.559923,(Cymbalaria_muralis:20.958033,(Linaria_vulgaris:17.181979,Misopates_orontium:17.181979)100/100:3.776054)100/100:11.509162)100/100:3.994336)100/100:8.051488,(Ligustrum_vulgare:10.945746,Syringa_vulgaris:10.945746)100/100:33.567273)100/100:20.571771,(((Calystegia_soldanella:3.579855,Convolvulus_arvensis:3.579855)100/100:52.707426,(Solanum_dulcamara:33.9,Solanum_nigrum:33.9)100/100:22.387282)100/100:8.171368,(((Sherardia_arvensis:10.071077,Cruciata_laevipes:10.071077)99/100:0.718559,(Galium_aparine:5.820074,Galium_uliginosum:5.820074)100/100:4.969561)100/100:51.291017,Pentaglottis_sempervirens:62.080652)97.7/100:2.377997)25.4/100:0.626141)100/100:14.17106,(Ilex_aquifolium:76.301337,(((Sambucus_nigra:57.517588,Succisa_pratensis:57.517588)100/100:10.981893,((Hedera_helix:23.895474,Hydrocotyle_vulgaris:23.895474)100/100:32.401643,(Torilis_japonica:47.955728,Lemna_minuta:47.955728)100/100:8.341389)100/100:12.202365)99.9/100:4.941505,(((((((((Tanacetum_vulgare:1.883357,Matricaria_discoidea:1.883357)100/100:12.813453,(((Filago_lutescens:2.051182,Logfia_minima:2.051182)99.5/100:1.325243,Pseudognaphalium_luteoalbum:3.376425)100/100:0.832552,Gnaphalium_uliginosum:4.208977)100/100:10.487833)55.9/100:0.731104,(Galatella_linosyris:2.031951,Tripolium_pannonicum:2.031951)100/100:13.395964)83.4/100:0.471253,Calendula_officinalis:15.899167)100/100:1.343607,(((Jacobaea_maritima:0.170628,Jacobaea_vulgaris:0.170628)100/100:2.866335,Senecio_sylvaticus:3.036963)100/100:2.563779,((Petasites_albus:0.699432,Petasites_hybridus:0.699432)99.6/100:1.822047,Tussilago_farfara:2.521478)100/100:3.079264)100/100:11.642032)60.1/100:0.449584,Pulicaria_dysenterica:17.692358)100/100:29.767642,(Lapsana_communis:19.616004,Tragopogon_pratensis:19.616004)100/100:27.843996)100/100:0.744442,(Carlina_vulgaris:27.231522,Carduus_nutans:27.231521)100/96:20.97292)100/100:20.815525,(Jasione_montana:50.514465,(Lobelia_dortmanna:16.881913,Lobelia_urens:16.881913)100/100:33.632552)100/100:18.505502)100/100:4.421019)100/100:2.860351)100/100:2.954513)100/100:10.224346,(((Calluna_vulgaris:66,Vaccinium_vitis_idaea:66)100/100:17.653826,((Primula_veris:4.051045,Primula_vulgaris:4.051045)100/100:54.432474,Samolus_valerandi:58.483519)100/100:25.170307)99.6/100:1.041034,(Impatiens_glandulifera:4.57351,Impatiens_parviflora:4.57351)100/100:80.12135)100/100:4.785337)99.7/100:1.057205,Cornus_suecica:90.537402)100/100:17.902662)100/100:4.559936)100/100:0.655197,Buxus_sempervirens:112.344803)100/100:0.210465,((((Aquilegia_vulgaris:19.005715,Thalictrum_minus:19.005715)100/100:36.994285,Adonis_annua:56)50.1/97:1.371605,(Ranunculus_sardous:13.020693,Ranunculus_sceleratus:13.020693)100/100:44.350912)100/100:23.370154,Berberis_vulgaris:80.741759)100/100:31.39258)100/100:0.407274,((Arctium_minus:61.330721,(Aponogeton_distachyos:44.508466,(Potamogeton_natans:35.699754,(Triglochin_maritima:2.813521,Triglochin_palustris:2.813521)100/100:32.886232)100/100:8.808712)100/100:16.822255)100/100:34.822361,(((((((((((((((Carex_sylvatica:3.773394,Carex_laevigata:3.773394)99.8/87:0.448946,Carex_pendula:4.22234)98.4/83:0.515513,(Carex_acutiformis:4.393076,Carex_nigra:4.393076)99.3/100:0.344776)100/100:1.728049,(Carex_distans:2.877016,Carex_extensa:2.877016)100/100:3.588885)100/100:0.52212,Carex_caryophyllea:6.988021)100/100:0.475314,((Carex_hirta:1.414105,(Carex_riparia:1.263119,Carex_rostrata:1.263119)58.2/100:0.150987)100/100:4.343099,Carex_depauperata:5.757205)100/100:1.706131)100/100:2.056601,(Carex_arenaria:3.264108,Carex_divulsa:3.264108)100/100:6.255829)100/100:4.8575,Trichophorum_cespitosum:14.377436)47.5/100:0.397285,(Eriophorum_vaginatum:2.486033,Scirpus_sylvaticus:2.486033)100/100:12.288688)100/100:17.056208,((Cyperus_fuscus:13.585069,(Schoenoplectus_lacustris:0.099874,Schoenoplectus_triqueter:0.099874)100/100:13.485195)100/100:6.251639,Eleocharis_quinqueflora:19.836708)100/100:11.994221)100/100:28.524794,((Juncus_effusus:20.474768,Juncus_squarrosus:20.474768)100/100:30.892241,(Luzula_pallescens:2.7799,Luzula_sylvatica:2.7799)100/100:48.58711)100/100:8.988714)100/100:19.555977,((Leersia_oryzoides:27.957844,((Bromus_sterilis:10.731085,Poa_chaixii:10.731085)100/100:3.539842,Polypogon_viridis:14.270927)100/100:13.686918)98.2/100:2.482156,(Digitaria_sanguinalis:14.387076,Phragmites_australis:14.387076)100/100:16.052924)100/100:49.471701)100/100:3.393692,Sparganium_emersum:83.305393)100/100:4.448853,Iris_foetidissima:87.754246)99.5/100:1.447792,Narthecium_ossifragum:89.202038)100/100:6.951044)100/100:15.573983)100/100:20.288928,((((((((((((Antitrichia_curtipendula:12.682685,Climacium_dendroides:12.682685)100/100:2.577706,Rhytidiadelphus_loreus:15.260391)99.2/69:0.575963,((Calliergon_cordifolium:4.966922,Straminergon_stramineum:4.966922)100/100:10.797725,(Cratoneuron_filicinum:13.840649,Thuidium_tamariscinum:13.840649)100/100:1.923997)23.3/69:0.071708)96.1/98:0.300961,(Hyocomium_armoricum:15.444711,((Pseudoscleropodium_purum:6.425543,Rhynchostegium_megapolitanum:6.425543)100/100:5.620511,Rhynchostegiella_tenella:12.046053)100/100:3.398658)100/98:0.692604)100/100:0.283842,(Hypnum_cupressiforme:14.945529,(Heterocladium_heteropterum:11.836218,Neckera_pumila:11.836218)100/100:3.109311)100/100:1.475628)100/100:1.125399,(Orthothecium_rufescens:14.389996,Pseudotaxiphyllum_elegans:14.389996)55.8/85:3.15656)99.9/90:2.457589,Plagiothecium_denticulatum:20.004145)99.4/90:5.772654,Isopterygiella_pulchella:25.776799)100/100:11.337191,Ulota_crispa:37.11399)100/100:10.146432,Bryoerythrophyllum_caledonicum:47.260422)100/100:20.306921,(Polytrichastrum_sexangulare:10.587015,(Polytrichum_commune:4.690111,Polytrichum_formosum:4.690111)100/100:5.896905)100/100:56.980328)100/100:14.642959,((Sphagnum_tenellum:2.113979,Sphagnum_contortum:2.113979)81.5/98:0.902369,Sphagnum_girgensohnii:3.016348)100/100:79.193953)100/100:9.227835)100/100:28.994936,Lunularia_cruciata:62.443201)100/100:0,Herbertus_hutchinsiae:62.443201)Root; `3b:[] 2f:{"id":"3f1f4ba0ccc299bd","slug":"lwcophylo","title":"lwCoPhylo","thumbnail":"4a28e48c95b49a6c4511ccb6ae825d372fd8b24fa9ac9cbb8b1c0f78481cfa50","access_level":"public","create_time":"$D2025-09-26T08:31:21.357Z","update_time":"$D2026-07-20T19:02:31.068Z","view_time":null,"first_public_time":"$D2025-09-26T14:26:19.211Z","fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"8736e7a8f8672f04","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":"starter_2024"},"version":273,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"448dbf923c3ebf2f","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":null}],"members":[{"type":"individual","id":"448dbf923c3ebf2f","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":null,"role":"editor"},{"type":"team","id":"8736e7a8f8672f04","login":"euphrasiologist","name":"Max Brown","avatar_url":"https://avatars-next.observableusercontent.com/592e4ba1993897720ef131d64a03c52cceee6126e1bc291cc61355043552c850","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"lwCoPhylo","cells":[{"id":0,"value":"# lwCoPhylo","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":5,"value":"Attempt to plot two trees against eachother. Tips have already been optimally rotated using `R::phytools::cophylo()` function.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":165,"value":"## Cophylo plot including ferns","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":197,"value":"### Nuclear vs mitochondria","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":207,"value":"Broadly very congruent!","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":199,"value":"nuclear_v_mito = cophylo({\n left: lw.rectangleLayout(lw.readTree(nuclear_mito)),\n right: lw.rectangleLayout(lw.readTree(mito_nuclear)),\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) =>\n 0.5 + (movedByLabel_nuc_mito.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel_nuc_mito.get(label)?.diff ?? 0) >= thresh\n ? \"#d62728\"\n : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":204,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":229,"value":"### Nuclear vs plastid","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":241,"value":"nuclear_v_plastid = cophylo({\n left: lw.rectangleLayout(lw.readTree(nuclear_plastid)),\n right: lw.rectangleLayout(lw.readTree(plastid_nuclear)),\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) =>\n 0.5 + (movedByLabel_nuc_plastid.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel_nuc_plastid.get(label)?.diff ?? 0) >= thresh\n ? \"#d62728\"\n : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":259,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":179,"value":"### Plastid vs mitochondria","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":47,"value":"chart = cophylo({\n left: mito_data,\n right: plastid_data,\n width: 600,\n height: 800,\n gap: 120,\n stroke: \"#666\",\n tipRadius: 0.5,\n linkStrokeWidth: (label) => 0.5 + (movedByLabel.get(label)?.norm ?? 0) * 4,\n linkStroke: (label) =>\n (movedByLabel.get(label)?.diff ?? 0) >= thresh ? \"#d62728\" : \"#bbb\",\n linkOpacity: 0.5\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":127,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":168,"value":"## Cophylo plot excluding ferns","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":183,"value":"### Plastid vs mitochondria","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":114,"value":"## Correlation in tip rank","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":116,"value":"// Spearman correlation of tip ranks\nfunction spearmanRankCorr(left, right) {\n const Ly = new Map(left.data.filter(d => d.isTip).map(d => [d.thisLabel, +d.y1]));\n const Ry = new Map(right.data.filter(d => d.isTip).map(d => [d.thisLabel, +d.y1]));\n const shared = [...Ly.keys()].filter(k => Ry.has(k));\n const x = shared.map(k => Ly.get(k));\n const y = shared.map(k => Ry.get(k));\n const mean = a => d3.mean(a);\n const sd = a => Math.sqrt(d3.variance(a));\n const cov = (a,b) => d3.mean(a.map((v,i) => (v-mean(a))*(b[i]-mean(b))));\n return cov(x,y) / (sd(x)*sd(y));\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":117,"value":"spearmanRankCorr(mito_data, plastid_data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":85,"value":"## The `cophylo` function","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":86,"value":"This takes two trees. I'd personally use `R::phytools::cophylo()` to compute these trees first.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":9,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":94,"value":"Optionally add tip movement.","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":121,"value":"viewof moved_table = Inputs.table(moved, {\n columns: [\"label\", \"y_left\", \"y_right\", \"diff\", \"signed\", \"norm\"],\n rows: 10\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":105,"value":"movedByLabel = new Map(moved.map(d => [d.label, d]));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":250,"value":"movedByLabel_nuc_mito = new Map(moved_nuc_mito.map(d => [d.label, d]));","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":253,"value":"movedByLabel_nuc_plastid = new Map(moved_nuc_plastid.map((d) => [d.label, d]))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":108,"value":"thresh = d3.quantile(moved.map((d) => d.diff).sort(d3.ascending), 0.9) ?? 0","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":96,"value":"moved = tipMovementByRank(mito_data, plastid_data)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":244,"value":"moved_nuc_mito = tipMovementByRank(\n lw.rectangleLayout(lw.readTree(nuclear_mito)),\n lw.rectangleLayout(lw.readTree(mito_nuclear))\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":247,"value":"moved_nuc_plastid = tipMovementByRank(\n lw.rectangleLayout(lw.readTree(nuclear_plastid)),\n lw.rectangleLayout(lw.readTree(plastid_nuclear))\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":88,"value":"function tipMovementByRank(left, right) {\n const Ly = new Map(\n left.data.filter((d) => d.isTip).map((d) => [d.thisLabel, +d.y1])\n );\n const Ry = new Map(\n right.data.filter((d) => d.isTip).map((d) => [d.thisLabel, +d.y1])\n );\n const shared = [...Ly.keys()].filter((k) => Ry.has(k));\n\n const rows = shared\n .map((label) => {\n const ly = Ly.get(label),\n ry = Ry.get(label);\n return {\n label,\n y_left: ly,\n y_right: ry,\n diff: Math.abs(ly - ry),\n signed: ly - ry\n };\n })\n .sort((a, b) => d3.descending(a.diff, b.diff));\n\n // add a normalized difference in [0,1]\n const n = rows.length || 1;\n for (const r of rows) r.norm = r.diff / (n - 1);\n return rows;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":99,"value":"## Data","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":25,"value":"mito_data = lw.rectangleLayout(lw.readTree(mito))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":12,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":21,"value":"plastid_data = lw.rectangleLayout(lw.readTree(plastid))","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":15,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":189,"value":"### The others","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":191,"value":"$37","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":194,"value":"$38","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":231,"value":"$39","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":238,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":103,"value":"## Imports","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined"},{"id":18,"value":"lw = import(\n \"https://unpkg.com/@euphrasiologist/lwphylo@1.1.5/src/index.js?module\"\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W3b","stdlib":"1","titling":"auto"}} 30:"$2f:body"