mbostock · May 5, 2021 09:30
diff --git a/.block b/.block
 license: gpl-3.0
 height: 960
 redirect: https://observablehq.com/@mbostock/tree-of-life
diff --git a/README.md b/README.md
diff --git a/index.html b/index.html
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 <label id="show-length">
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 <!-- Copyright 2011 Jason Davies https://github.com/jasondavies/newick.js -->
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diff --git a/life.txt b/life.txt
 (((((((((((((((((((Escherichia_coli_EDL933:0.00000,Escherichia_coli_O157_H7:0.00000)Escherichia_subclade:0.00044[96],((Escherichia_coli_O6:0.00000,Escherichia_coli_K12:0.00022)Escherichia_subclade:0.00022[76],(Shigella_flexneri_2a_2457T:0.00000,Shigella_flexneri_2a_301:0.00000)Shigella:0.00266[100])Enterobacteriaceae_subclade:0.00000[75])Enterobacteriaceae_subclade:0.00813[100],((Salmonella_enterica:0.00000,Salmonella_typhi:0.00000)Salmonella_subclade:0.00146[100],Salmonella_typhimurium:0.00075)Salmonella:0.00702[100])Enterobacteriaceae_subclade:0.03131[100],((Yersinia_pestis_Medievalis:0.00000,(Yersinia_pestis_KIM:0.00000,Yersinia_pestis_CO92:0.00000)Yersinia_subclade:0.00000[31])Yersinia:0.03398[100],Photorhabdus_luminescens:0.05076)Enterobacteriaceae_subclade:0.01182[61])Enterobacteriaceae_subclade:0.02183[98],((Blochmannia_floridanus:0.32481,Wigglesworthia_brevipalpis:0.35452)Enterobacteriaceae_subclade:0.08332[100],(Buchnera_aphidicola_Bp:0.27492,(Buchnera_aphidicola_APS:0.09535,Buchnera_aphidicola_Sg:0.10235)Buchnera_subclade:0.10140[100])Buchnera:0.06497[100])Enterobacteriaceae_subclade:0.15030[100])Enterobacteriaceae:0.02808[100],((Pasteurella_multocida:0.03441,Haemophilus_influenzae:0.03754)Pasteurellaceae_subclade:0.01571[94],Haemophilus_ducreyi:0.05333)Pasteurellaceae:0.07365[100])Gammaproteobacteria_subclade:0.03759[100],((((Vibrio_vulnificus_YJ016:0.00021,Vibrio_vulnificus_CMCP6:0.00291)Vibrio_subclade:0.01212[100],Vibrio_parahaemolyticus:0.01985)Vibrio_subclade:0.01536[100],Vibrio_cholerae:0.02995)Vibrio:0.02661[100],Photobacterium_profundum:0.06131)Vibrionaceae:0.05597[100])Gammaproteobacteria_subclade:0.03492[81],Shewanella_oneidensis:0.10577)Gammaproteobacteria_subclade:0.12234[100],((Pseudomonas_putida:0.02741,Pseudomonas_syringae:0.03162)Pseudomonas_subclade:0.02904[100],Pseudomonas_aeruginosa:0.03202)Pseudomonas:0.14456[100])Gammaproteobacteria_subclade:0.04492[98],((Xylella_fastidiosa_700964:0.01324,Xylella_fastidiosa_9a5c:0.00802)Xylella:0.10192[100],(Xanthomonas_axonopodis:0.01069,Xanthomonas_campestris:0.00934)Xanthomonas:0.05037[100])Xanthomonadaceae:0.24151[100])Gammaproteobacteria_subclade:0.02475[49],Coxiella_burnetii:0.33185)Gammaproteobacteria:0.03328[54],((((Neisseria_meningitidis_A:0.00400,Neisseria_meningitidis_B:0.00134)Neisseria:0.12615[100],Chromobacterium_violaceum:0.09623)Neisseriaceae:0.07131[100],((Bordetella_pertussis:0.00127,(Bordetella_parapertussis:0.00199,Bordetella_bronchiseptica:0.00022)Bordetella_subclade:0.00006[67])Bordetella:0.14218[100],Ralstonia_solanacearum:0.11464)Burkholderiales:0.08478[100])Betaproteobacteria_subclade:0.03840[75],Nitrosomonas_europaea:0.22059)Betaproteobacteria:0.08761[100])Proteobacteria_subclade:0.16913[100],((((((Agrobacterium_tumefaciens_Cereon:0.00000,Agrobacterium_tumefaciens_WashU:0.00000):0.05735[100],Rhizobium_meliloti:0.05114)Sinorhizobium:0.05575[100],((Brucella_suis:0.00102,Brucella_melitensis:0.00184)Brucella:0.08660[100],Rhizobium_loti:0.09308)Rhizobiales_subclade:0.02384[51])Rhizobiales_subclade:0.08637[100],(Rhodopseudomonas_palustris:0.04182,Bradyrhizobium_japonicum:0.06346)Bradyrhizobiaceae:0.14122[100])Rhizobiales:0.05767[100],Caulobacter_crescentus:0.23943)Alphaproteobacteria_subclade:0.11257[100],(Wolbachia_sp._wMel:0.51596,(Rickettsia_prowazekii:0.04245,Rickettsia_conorii:0.02487)Rickettsia:0.38019[100])Rickettsiaceae:0.12058[100])Alphaproteobacteria:0.12365[100])Proteobacteria_subclade:0.06301[100],((((Helicobacter_pylori_J99:0.00897,Helicobacter_pylori_26695:0.00637)Helicobacter_subclade:0.19055[100],Helicobacter_hepaticus:0.12643)Helicobacter:0.05330[100],Wolinella_succinogenes:0.11644)Helicobacteraceae:0.09105[100],Campylobacter_jejuni:0.20399)Campylobacterales:0.41390[100])Proteobacteria_subclade:0.04428[82],((Desulfovibrio_vulgaris:0.38320,(Geobacter_sulfurreducens:0.22491,Bdellovibrio_bacteriovorus:0.45934)Deltaproteobacteria_subclade:0.04870[43])Deltaproteobacteria:0.04100[69],(Acidobacterium_capsulatum:0.24572,Solibacter_usitatus:0.29086)Acidobacteria:0.20514[100])Bacteria_subclade:0.04214[64])Bacteria_subclade:0.05551[98],((Fusobacterium_nucleatum:0.45615,(Aquifex_aeolicus:0.40986,Thermotoga_maritima:0.34182)Bacteria_subclade:0.07696[100])Bacteria_subclade:0.03606[35],(((Thermus_thermophilus:0.26583,Deinococcus_radiodurans:0.29763)Deinococci:0.24776[100],Dehalococcoides_ethenogenes:0.53988)Bacteria_subclade:0.04370[35],((((Nostoc_sp._PCC_7120:0.12014,Synechocystis_sp._PCC6803:0.15652)Cyanobacteria_subclade:0.04331[98],Synechococcus_elongatus:0.13147)Cyanobacteria_subclade:0.05040[100],(((Synechococcus_sp._WH8102:0.06780,Prochlorococcus_marinus_MIT9313:0.05434)Cyanobacteria_subclade:0.04879[100],Prochlorococcus_marinus_SS120:0.10211)Cyanobacteria_subclade:0.04238[74],Prochlorococcus_marinus_CCMP1378:0.16170)Cyanobacteria_subclade:0.20442[100])Cyanobacteria_subclade:0.07646[100],Gloeobacter_violaceus:0.23764)Cyanobacteria:0.24501[100])Bacteria_subclade:0.04332[39])Bacteria_subclade:0.02720[51])Bacteria_subclade:0.03471[74],((((Gemmata_obscuriglobus:0.36751,Rhodopirellula_baltica:0.38017)Planctomycetaceae:0.24062[100],((Leptospira_interrogans_L1-130:0.00000,Leptospira_interrogans_56601:0.00027)Leptospira:0.47573[100],((Treponema_pallidum:0.25544,Treponema_denticola:0.16072)Treponema:0.19057[100],Borrelia_burgdorferi:0.42323)Spirochaetaceae:0.20278[100])Spirochaetales:0.07248[95])Bacteria_subclade:0.04615[42],(((Tropheryma_whipplei_TW08/27:0.00009,Tropheryma_whipplei_Twist:0.00081)Tropheryma:0.44723[100],Bifidobacterium_longum:0.29283)Actinobacteridae_subclade:0.14429[100],(((((Corynebacterium_glutamicum_13032:0.00022,Corynebacterium_glutamicum:0.00000)Corynebacterium_subclade:0.03415[100],Corynebacterium_efficiens:0.02559)Corynebacterium_subclade:0.03682[100],Corynebacterium_diphtheriae:0.06479)Corynebacterium:0.13907[100],(((Mycobacterium_bovis:0.00067,(Mycobacterium_tuberculosis_CDC1551:0.00000,Mycobacterium_tuberculosis_H37Rv:0.00000)Mycobacterium_subclade:0.00022[98])Mycobacterium_subclade:0.03027[100],Mycobacterium_leprae:0.05135)Mycobacterium_subclade:0.01514[97],Mycobacterium_paratuberculosis:0.02091)Mycobacterium:0.11523[100])Corynebacterineae:0.09883[100],(Streptomyces_avermitilis:0.02680,Streptomyces_coelicolor:0.02678)Streptomyces:0.16707[100])Actinomycetales_subclade:0.06110[91])Actinobacteridae:0.26800[100])Bacteria_subclade:0.03480[23],((Fibrobacter_succinogenes:0.51984,(Chlorobium_tepidum:0.37204,(Porphyromonas_gingivalis:0.11304,Bacteroides_thetaiotaomicron:0.13145)Bacteroidales:0.34694[100])Bacteroidetes/Chlorobi_group:0.09237[100])Bacteria_subclade:0.04841[62],(((Chlamydophila_pneumoniae_TW183:0.00000,(Chlamydia_pneumoniae_J138:0.00000,(Chlamydia_pneumoniae_CWL029:0.00000,Chlamydia_pneumoniae_AR39:0.00000)Chlamydophila_subclade:0.00000[37])Chlamydophila_subclade:0.00000[44])Chlamydophila_subclade:0.10482[100],Chlamydophila_caviae:0.05903)Chlamydophila:0.04170[98],(Chlamydia_muridarum:0.01938,Chlamydia_trachomatis:0.02643)Chlamydia:0.06809[100])Chlamydiaceae:0.60169[100])Bacteria_subclade:0.04443[32])Bacteria_subclade:0.04284[67])Bacteria_subclade:0.02646[66],((Thermoanaerobacter_tengcongensis:0.17512,((Clostridium_tetani:0.10918,Clostridium_perfringens:0.11535)Clostridium_subclade:0.03238[78],Clostridium_acetobutylicum:0.11396)Clostridium:0.15056[100])Clostridia:0.11788[100],(((((Mycoplasma_mobile:0.27702,Mycoplasma_pulmonis:0.28761)Mycoplasma_subclade:0.28466[100],((((Mycoplasma_pneumoniae:0.10966,Mycoplasma_genitalium:0.11268)Mycoplasma_subclade:0.31768[100],Mycoplasma_gallisepticum:0.24373)Mycoplasma_subclade:0.14180[100],Mycoplasma_penetrans:0.34890)Mycoplasma_subclade:0.06674[94],Ureaplasma_parvum:0.33874)Mycoplasmataceae_subclade:0.19177[100])Mycoplasmataceae_subclade:0.07341[100],Mycoplasma_mycoides:0.37680)Mycoplasmataceae:0.12541[100],Phytoplasma_Onion_yellows:0.47843)Mollicutes:0.09099[100],(((((Listeria_monocytogenes_F2365:0.00063,Listeria_monocytogenes_EGD:0.00144)Listeria_subclade:0.00235[90],Listeria_innocua:0.00248)Listeria:0.13517[100],((Oceanobacillus_iheyensis:0.13838,Bacillus_halodurans:0.09280)Bacillaceae_subclade:0.02676[91],(((Bacillus_cereus_ATCC_14579:0.00342,Bacillus_cereus_ATCC_10987:0.00123)Bacillus_subclade:0.00573[100],Bacillus_anthracis:0.00331)Bacillus_subclade:0.08924[100],Bacillus_subtilis:0.07876)Bacillus:0.01984[96])Bacillaceae:0.03907[100])Bacillales_subclade:0.02816[69],((Staphylococcus_aureus_MW2:0.00000,(Staphylococcus_aureus_N315:0.00022,Staphylococcus_aureus_Mu50:0.00022)Staphylococcus_subclade:0.00022[61])Staphylococcus_subclade:0.02479[100],Staphylococcus_epidermidis:0.03246)Staphylococcus:0.17366[100])Bacillales:0.02828[64],(((((((Streptococcus_agalactiae_III:0.00110,Streptococcus_agalactiae_V:0.00155)Streptococcus_subclade:0.01637[100],(Streptococcus_pyogenes_M1:0.00134,(Streptococcus_pyogenes_MGAS8232:0.00045,(Streptococcus_pyogenes_MGAS315:0.00000,Streptococcus_pyogenes_SSI-1:0.00022)Streptococcus_subclade:0.00110[100])Streptococcus_subclade:0.00066[87])Streptococcus_subclade:0.02250[100])Streptococcus_subclade:0.01360[100],Streptococcus_mutans:0.04319)Streptococcus_subclade:0.01920[99],(Streptococcus_pneumoniae_R6:0.00119,Streptococcus_pneumoniae_TIGR4:0.00124)Streptococcus_subclade:0.03607[100])Streptococcus:0.04983[100],Lactococcus_lactis:0.11214)Streptococcaceae:0.08901[100],Enterococcus_faecalis:0.07946)Lactobacillales_subclade:0.03958[100],(Lactobacillus_johnsonii:0.20999,Lactobacillus_plantarum:0.14371)Lactobacillus:0.06763[100])Lactobacillales:0.08989[100])Bacilli:0.08905[100])Firmicutes_subclade:0.09540[92])Firmicutes:0.04315[54])Bacteria:1.34959,(((((Thalassiosira_pseudonana:0.33483,(Cryptosporidium_hominis:0.25048,Plasmodium_falciparum:0.28267)Apicomplexa:0.14359[100])Eukaryota_subclade:0.03495[42],(((Oryza_sativa:0.07623,Arabidopsis_thaliana:0.09366)Streptophyta:0.15770[100],Cyanidioschyzon_merolae:0.38319)Eukaryota_subclade:0.08133[96],(Dictyostelium_discoideum:0.34685,(((Eremothecium_gossypii:0.07298,Saccharomyces_cerevisiae:0.07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diff --git a/thumbnail.png b/thumbnail.png
	license: gpl-3.0
	height: 960
	redirect: https://observablehq.com/@mbostock/tree-of-life
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	.labels {
	font: 10px sans-serif;
	}

	.link--active {
	stroke: #000 !important;
	stroke-width: 1.5px;
	}

	.link-extension--active {
	stroke-opacity: .6;
	}

	.label--active {
	font-weight: bold;
	}

	</style>
	<label id="show-length">
	<input type="checkbox"> Show branch length
	</label>

	<!-- Copyright 2011 Jason Davies https://github.com/jasondavies/newick.js -->
	<script>function parseNewick(a){for(var e=[],r={},s=a.split(/\s(;\|\(\|\)\|,\|:)\s/),t=0;t<s.length;t++){var n=s[t];switch(n){case"(":var c={};r.branchset=[c],e.push(r),r=c;break;case",":var c={};e[e.length-1].branchset.push(c),r=c;break;case")":r=e.pop();break;case":":break;default:var h=s[t-1];")"==h\|\|"("==h\|\|","==h?r.name=n:":"==h&&(r.length=parseFloat(n))}}return r}</script>

	<!-- Copyright 2016 Mike Bostock https://d3js.org -->
	<script src="https://d3js.org/d3.v4.min.js"></script>
	<script>

	var outerRadius = 960 / 2,
	innerRadius = outerRadius - 170;

	var color = d3.scaleOrdinal()
	.domain(["Bacteria", "Eukaryota", "Archaea"])
	.range(d3.schemeCategory10);

	var cluster = d3.cluster()
	.size([360, innerRadius])
	.separation(function(a, b) { return 1; });

	var svg = d3.select("body").append("svg")
	.attr("width", outerRadius * 2)
	.attr("height", outerRadius * 2);

	var legend = svg.append("g")
	.attr("class", "legend")
	.selectAll("g")
	.data(color.domain())
	.enter().append("g")
	.attr("transform", function(d, i) { return "translate(" + (outerRadius * 2 - 10) + "," + (i * 20 + 10) + ")"; });

	legend.append("rect")
	.attr("x", -18)
	.attr("width", 18)
	.attr("height", 18)
	.attr("fill", color);

	legend.append("text")
	.attr("x", -24)
	.attr("y", 9)
	.attr("dy", ".35em")
	.attr("text-anchor", "end")
	.text(function(d) { return d; });

	var chart = svg.append("g")
	.attr("transform", "translate(" + outerRadius + "," + outerRadius + ")");

	d3.text("life.txt", function(error, life) {
	if (error) throw error;

	var root = d3.hierarchy(parseNewick(life), function(d) { return d.branchset; })
	.sum(function(d) { return d.branchset ? 0 : 1; })
	.sort(function(a, b) { return (a.value - b.value) \|\| d3.ascending(a.data.length, b.data.length); });

	cluster(root);

	var input = d3.select("#show-length input").on("change", changed),
	timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

	setRadius(root, root.data.length = 0, innerRadius / maxLength(root));
	setColor(root);

	var linkExtension = chart.append("g")
	.attr("class", "link-extensions")
	.selectAll("path")
	.data(root.links().filter(function(d) { return !d.target.children; }))
	.enter().append("path")
	.each(function(d) { d.target.linkExtensionNode = this; })
	.attr("d", linkExtensionConstant);

	var link = chart.append("g")
	.attr("class", "links")
	.selectAll("path")
	.data(root.links())
	.enter().append("path")
	.each(function(d) { d.target.linkNode = this; })
	.attr("d", linkConstant)
	.attr("stroke", function(d) { return d.target.color; });

	chart.append("g")
	.attr("class", "labels")
	.selectAll("text")
	.data(root.leaves())
	.enter().append("text")
	.attr("dy", ".31em")
	.attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
	.attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
	.text(function(d) { return d.data.name.replace(/_/g, " "); })
	.on("mouseover", mouseovered(true))
	.on("mouseout", mouseovered(false));

	function changed() {
	clearTimeout(timeout);
	var t = d3.transition().duration(750);
	linkExtension.transition(t).attr("d", this.checked ? linkExtensionVariable : linkExtensionConstant);
	link.transition(t).attr("d", this.checked ? linkVariable : linkConstant);
	}

	function mouseovered(active) {
	return function(d) {
	d3.select(this).classed("label--active", active);
	d3.select(d.linkExtensionNode).classed("link-extension--active", active).each(moveToFront);
	do d3.select(d.linkNode).classed("link--active", active).each(moveToFront); while (d = d.parent);
	};
	}

	function moveToFront() {
	this.parentNode.appendChild(this);
	}
	});

	// Compute the maximum cumulative length of any node in the tree.
	function maxLength(d) {
	return d.data.length + (d.children ? d3.max(d.children, maxLength) : 0);
	}

	// Set the radius of each node by recursively summing and scaling the distance from the root.
	function setRadius(d, y0, k) {
	d.radius = (y0 += d.data.length) * k;
	if (d.children) d.children.forEach(function(d) { setRadius(d, y0, k); });
	}

	// Set the color of each node by recursively inheriting.
	function setColor(d) {
	var name = d.data.name;
	d.color = color.domain().indexOf(name) >= 0 ? color(name) : d.parent ? d.parent.color : null;
	if (d.children) d.children.forEach(setColor);
	}

	function linkVariable(d) {
	return linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius);
	}

	function linkConstant(d) {
	return linkStep(d.source.x, d.source.y, d.target.x, d.target.y);
	}

	function linkExtensionVariable(d) {
	return linkStep(d.target.x, d.target.radius, d.target.x, innerRadius);
	}

	function linkExtensionConstant(d) {
	return linkStep(d.target.x, d.target.y, d.target.x, innerRadius);
	}

	// Like d3.svg.diagonal.radial, but with square corners.
	function linkStep(startAngle, startRadius, endAngle, endRadius) {
	var c0 = Math.cos(startAngle = (startAngle - 90) / 180 * Math.PI),
	s0 = Math.sin(startAngle),
	c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI),
	s1 = Math.sin(endAngle);
	return "M" + startRadius * c0 + "," + startRadius * s0
	+ (endAngle === startAngle ? "" : "A" + startRadius + "," + startRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
	+ "L" + endRadius * c1 + "," + endRadius * s1;
	}

	</script>