Skip to content

Instantly share code, notes, and snippets.

@mbostock

mbostock/.block

Last active May 5, 2021 09:30
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save mbostock/c034d66572fd6bd6815a to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save mbostock/c034d66572fd6bd6815a to your computer and use it in GitHub Desktop.
Download ZIP

Revisions

  1. mbostock revised this gist Feb 26, 2019. 1 changed file with 1 addition and 1 deletion.
    2 changes: 1 addition & 1 deletion .block
    View file
    Original file line number Diff line number Diff line change
    @@ -1,3 +1,3 @@
    license: gpl-3.0
    height: 960
    redirect: https://beta.observablehq.com/@mbostock/tree-of-life
    redirect: https://observablehq.com/@mbostock/tree-of-life
  2. mbostock revised this gist Oct 25, 2018. 1 changed file with 1 addition and 0 deletions.
    1 change: 1 addition & 0 deletions .block
    View file
    Original file line number Diff line number Diff line change
    @@ -1,2 +1,3 @@
    license: gpl-3.0
    height: 960
    redirect: https://beta.observablehq.com/@mbostock/tree-of-life
  3. mbostock revised this gist Jan 13, 2017. 2 changed files with 50 additions and 35 deletions.
    1 change: 1 addition & 0 deletions .block
    View file
    Original file line number Diff line number Diff line change
    @@ -1 +1,2 @@
    license: gpl-3.0
    height: 960
    84 changes: 49 additions & 35 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -49,21 +49,19 @@
    <!-- 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 2015 Mike Bostock http://d3js.org -->
    <script src="//d3js.org/d3.v3.min.js"></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.scale.category10()
    .domain(["Bacteria", "Eukaryota", "Archaea"]);
    var color = d3.scaleOrdinal()
    .domain(["Bacteria", "Eukaryota", "Archaea"])
    .range(d3.schemeCategory10);

    var cluster = d3.layout.cluster()
    var cluster = d3.cluster()
    .size([360, innerRadius])
    .children(function(d) { return d.branchset; })
    .value(function(d) { return 1; })
    .sort(function(a, b) { return (a.value - b.value) || d3.ascending(a.length, b.length); })
    .separation(function(a, b) { return 1; });

    var svg = d3.select("body").append("svg")
    @@ -73,21 +71,21 @@
    var legend = svg.append("g")
    .attr("class", "legend")
    .selectAll("g")
    .data(color.domain())
    .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)
    .style("fill", color);
    .attr("fill", color);

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

    var chart = svg.append("g")
    @@ -96,51 +94,52 @@
    d3.text("life.txt", function(error, life) {
    if (error) throw error;

    var root = parseNewick(life),
    nodes = cluster.nodes(root),
    links = cluster.links(nodes),
    input = d3.select("#show-length input").on("change", changed),
    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.length = 0, innerRadius / maxLength(root));
    setRadius(root, root.data.length = 0, innerRadius / maxLength(root));
    setColor(root);

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

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

    chart.append("g")
    .attr("class", "labels")
    .selectAll("text")
    .data(nodes.filter(function(d) { return !d.children; }))
    .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)"); })
    .style("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
    .text(function(d) { return d.name.replace(/_/g, " "); })
    .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 checked = this.checked;
    d3.transition().duration(750).each(function() {
    linkExtension.transition().attr("d", function(d) { return step(d.target.x, checked ? d.target.radius : d.target.y, d.target.x, innerRadius); });
    link.transition().attr("d", function(d) { return step(d.source.x, checked ? d.source.radius : d.source.y, d.target.x, checked ? d.target.radius : d.target.y) });
    });
    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) {
    @@ -158,23 +157,40 @@

    // Compute the maximum cumulative length of any node in the tree.
    function maxLength(d) {
    return d.length + (d.children ? d3.max(d.children, maxLength) : 0);
    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.length) * 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) {
    d.color = color.domain().indexOf(d.name) >= 0 ? color(d.name) : d.parent ? d.parent.color : null;
    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 step(startAngle, startRadius, endAngle, endRadius) {
    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),
    @@ -184,6 +200,4 @@
    + "L" + endRadius * c1 + "," + endRadius * s1;
    }

    d3.select(self.frameElement).style("height", outerRadius * 2 + "px");

    </script>
  4. mbostock revised this gist Feb 9, 2016. 1 changed file with 1 addition and 0 deletions.
    1 change: 1 addition & 0 deletions .block
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1 @@
    license: gpl-3.0
  5. mbostock revised this gist Oct 31, 2015. 1 changed file with 1 addition and 1 deletion.
    2 changes: 1 addition & 1 deletion index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -50,7 +50,7 @@
    <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 2015 Mike Bostock http://d3js.org -->
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js" charset="utf-8"></script>
    <script src="//d3js.org/d3.v3.min.js"></script>
    <script>

    var outerRadius = 960 / 2,
  6. mbostock revised this gist Oct 20, 2015. 1 changed file with 0 additions and 0 deletions.
    Binary file modified thumbnail.png
    View file
    Loading
    Sorry, something went wrong. Reload?
    Sorry, we cannot display this file.
    Sorry, this file is invalid so it cannot be displayed.
  7. mbostock revised this gist Oct 20, 2015. 1 changed file with 1 addition and 0 deletions.
    1 change: 1 addition & 0 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -4,6 +4,7 @@

    body {
    font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
    margin: 0;
    }

    #show-length {
  8. mbostock revised this gist Oct 20, 2015. 1 changed file with 15 additions and 11 deletions.
    26 changes: 15 additions & 11 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -12,18 +12,18 @@
    left: 10px;
    }

    .link {
    .links {
    fill: none;
    stroke: #000;
    }

    .link-extension {
    .link-extensions {
    fill: none;
    stroke: #000;
    stroke-opacity: .25;
    }

    .label {
    .labels {
    font: 10px sans-serif;
    }

    @@ -69,10 +69,11 @@
    .attr("width", outerRadius * 2)
    .attr("height", outerRadius * 2);

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

    legend.append("rect")
    @@ -103,25 +104,28 @@
    setRadius(root, root.length = 0, innerRadius / maxLength(root));
    setColor(root);

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

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

    chart.append("g").selectAll(".label")
    chart.append("g")
    .attr("class", "labels")
    .selectAll("text")
    .data(nodes.filter(function(d) { return !d.children; }))
    .enter().append("text")
    .attr("class", "label")
    .attr("dy", ".31em")
    .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
    .style("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
  9. mbostock revised this gist Oct 20, 2015. 1 changed file with 2 additions and 2 deletions.
    4 changes: 2 additions & 2 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -100,7 +100,7 @@
    input = d3.select("#show-length input").on("change", changed),
    timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

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

    var linkExtension = chart.append("g").selectAll(".link-extension")
    @@ -153,7 +153,7 @@

    // Compute the maximum cumulative length of any node in the tree.
    function maxLength(d) {
    return (d.length || (d.length = 0)) + (d.children ? d3.max(d.children, maxLength) : 0);
    return d.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.
  10. mbostock revised this gist Oct 20, 2015. 1 changed file with 1 addition and 1 deletion.
    2 changes: 1 addition & 1 deletion index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -73,7 +73,7 @@
    .data(color.domain())
    .enter().append("g")
    .attr("class", "legend")
    .attr("transform", function(d, i) { return "translate(" + outerRadius * 2 + "," + (i * 20 + 2) + ")"; });
    .attr("transform", function(d, i) { return "translate(" + (outerRadius * 2 - 10) + "," + (i * 20 + 10) + ")"; });

    legend.append("rect")
    .attr("x", -18)
  11. mbostock revised this gist Oct 20, 2015. 1 changed file with 47 additions and 13 deletions.
    60 changes: 47 additions & 13 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -2,8 +2,11 @@
    <meta charset="utf-8">
    <style>

    #show-length {
    body {
    font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
    }

    #show-length {
    position: absolute;
    top: 10px;
    left: 10px;
    @@ -25,16 +28,15 @@
    }

    .link--active {
    stroke: #f00;
    stroke: #000 !important;
    stroke-width: 1.5px;
    }

    .link-extension--active {
    stroke: #f00;
    stroke-opacity: .6;
    }

    .label--active {
    fill: #f00;
    font-weight: bold;
    }

    @@ -53,6 +55,9 @@
    var outerRadius = 960 / 2,
    innerRadius = outerRadius - 170;

    var color = d3.scale.category10()
    .domain(["Bacteria", "Eukaryota", "Archaea"]);

    var cluster = d3.layout.cluster()
    .size([360, innerRadius])
    .children(function(d) { return d.branchset; })
    @@ -62,8 +67,28 @@

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

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

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

    legend.append("text")
    .attr("x", -24)
    .attr("y", 9)
    .attr("dy", ".35em")
    .style("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) {
    @@ -75,23 +100,25 @@
    input = d3.select("#show-length input").on("change", changed),
    timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

    adjustRadius(root, 0, innerRadius / maxLength(root));
    setRadius(root, 0, innerRadius / maxLength(root));
    setColor(root);

    var linkExtension = svg.append("g").selectAll(".link-extension")
    var linkExtension = chart.append("g").selectAll(".link-extension")
    .data(links.filter(function(d) { return !d.target.children; }))
    .enter().append("path")
    .each(function(d) { d.target.linkExtensionNode = this; })
    .attr("class", "link-extension")
    .attr("d", function(d) { return step(d.target.x, d.target.y, d.target.x, innerRadius); });

    var link = svg.append("g").selectAll(".link")
    var link = chart.append("g").selectAll(".link")
    .data(links)
    .enter().append("path")
    .each(function(d) { d.target.linkNode = this; })
    .attr("class", "link")
    .attr("d", function(d) { return step(d.source.x, d.source.y, d.target.x, d.target.y) });
    .attr("d", function(d) { return step(d.source.x, d.source.y, d.target.x, d.target.y) })
    .style("stroke", function(d) { return d.target.color; });

    svg.append("g").selectAll(".label")
    chart.append("g").selectAll(".label")
    .data(nodes.filter(function(d) { return !d.children; }))
    .enter().append("text")
    .attr("class", "label")
    @@ -130,8 +157,15 @@
    }

    // Set the radius of each node by recursively summing and scaling the distance from the root.
    function adjustRadius(d, y0, k) {
    d.radius = (y0 += d.length) * k, d.children && d.children.forEach(function(d) { adjustRadius(d, y0, k); });
    function setRadius(d, y0, k) {
    d.radius = (y0 += d.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) {
    d.color = color.domain().indexOf(d.name) >= 0 ? color(d.name) : d.parent ? d.parent.color : null;
    if (d.children) d.children.forEach(setColor);
    }

    // Like d3.svg.diagonal.radial, but with square corners.
  12. mbostock revised this gist Oct 20, 2015. 1 changed file with 11 additions and 11 deletions.
    22 changes: 11 additions & 11 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -56,7 +56,8 @@
    var cluster = d3.layout.cluster()
    .size([360, innerRadius])
    .children(function(d) { return d.branchset; })
    .sort(function(a, b) { return d3.ascending(a.name, b.name); })
    .value(function(d) { return 1; })
    .sort(function(a, b) { return (a.value - b.value) || d3.ascending(a.length, b.length); })
    .separation(function(a, b) { return 1; });

    var svg = d3.select("body").append("svg")
    @@ -71,11 +72,10 @@
    var root = parseNewick(life),
    nodes = cluster.nodes(root),
    links = cluster.links(nodes),
    scale = innerRadius / maxDepth(root),
    input = d3.select("#show-length input").on("change", changed),
    timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

    adjustDepth(root, 0);
    adjustRadius(root, 0, innerRadius / maxLength(root));

    var linkExtension = svg.append("g").selectAll(".link-extension")
    .data(links.filter(function(d) { return !d.target.children; }))
    @@ -106,8 +106,8 @@
    clearTimeout(timeout);
    var checked = this.checked;
    d3.transition().duration(750).each(function() {
    linkExtension.transition().attr("d", function(d) { return step(d.target.x, checked ? d.target.depth * scale : d.target.y, d.target.x, innerRadius); });
    link.transition().attr("d", function(d) { return step(d.source.x, checked ? d.source.depth * scale : d.source.y, d.target.x, checked ? d.target.depth * scale : d.target.y) });
    linkExtension.transition().attr("d", function(d) { return step(d.target.x, checked ? d.target.radius : d.target.y, d.target.x, innerRadius); });
    link.transition().attr("d", function(d) { return step(d.source.x, checked ? d.source.radius : d.source.y, d.target.x, checked ? d.target.radius : d.target.y) });
    });
    }

    @@ -124,14 +124,14 @@
    }
    });

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

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

    // Like d3.svg.diagonal.radial, but with square corners.
  13. mbostock revised this gist Oct 20, 2015. 2 changed files with 3 additions and 2 deletions.
    3 changes: 2 additions & 1 deletion index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -56,6 +56,7 @@
    var cluster = d3.layout.cluster()
    .size([360, innerRadius])
    .children(function(d) { return d.branchset; })
    .sort(function(a, b) { return d3.ascending(a.name, b.name); })
    .separation(function(a, b) { return 1; });

    var svg = d3.select("body").append("svg")
    @@ -97,7 +98,7 @@
    .attr("dy", ".31em")
    .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
    .style("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
    .text(function(d) { return d.name; })
    .text(function(d) { return d.name.replace(/_/g, " "); })
    .on("mouseover", mouseovered(true))
    .on("mouseout", mouseovered(false));

    2 changes: 1 addition & 1 deletion life.txt
    View file
    Original file line number Diff line number Diff line change
    @@ -1 +1 @@
    (((((((((((((((((((Escherichia coli EDL933:0.00000,Escherichia coli O157 H7:0.00000)96:0.00044,((Escherichia coli O6:0.00000,Escherichia coli K12:0.00022)76:0.00022,(Shigella flexneri 2a 2457T:0.00000,Shigella flexneri 2a 301:0.00000)100:0.00266)75:0.00000)100:0.00813,((Salmonella enterica:0.00000,Salmonella typhi:0.00000)100:0.00146,Salmonella typhimurium:0.00075)100:0.00702)100:0.03131,((Yersinia pestis Medievalis:0.00000,(Yersinia pestis KIM:0.00000,Yersinia pestis CO92:0.00000)31:0.00000)100:0.03398,Photorhabdus luminescens:0.05076)61:0.01182)98:0.02183,((Blochmannia floridanus:0.32481,Wigglesworthia brevipalpis:0.35452)100:0.08332,(Buchnera aphidicola Bp:0.27492,(Buchnera aphidicola APS:0.09535,Buchnera aphidicola Sg:0.10235)100:0.10140)100:0.06497)100:0.15030)100:0.02808,((Pasteurella multocida:0.03441,Haemophilus influenzae:0.03754)94:0.01571,Haemophilus ducreyi:0.05333)100:0.07365)100:0.03759,((((Vibrio vulnificus YJ016:0.00021,Vibrio vulnificus CMCP6:0.00291)100:0.01212,Vibrio parahaemolyticus:0.01985)100:0.01536,Vibrio cholerae:0.02995)100:0.02661,Photobacterium profundum:0.06131)100:0.05597)81:0.03492,Shewanella oneidensis:0.10577)100:0.12234,((Pseudomonas putida:0.02741,Pseudomonas syringae:0.03162)100:0.02904,Pseudomonas aeruginosa:0.03202)100:0.14456)98:0.04492,((Xylella fastidiosa 700964:0.01324,Xylella fastidiosa 9a5c:0.00802)100:0.10192,(Xanthomonas axonopodis:0.01069,Xanthomonas campestris:0.00934)100:0.05037)100:0.24151)49:0.02475,Coxiella burnetii:0.33185)54:0.03328,((((Neisseria meningitidis A:0.00400,Neisseria meningitidis B:0.00134)100:0.12615,Chromobacterium violaceum:0.09623)100:0.07131,((Bordetella pertussis:0.00127,(Bordetella parapertussis:0.00199,Bordetella bronchiseptica:0.00022)67:0.00006)100:0.14218,Ralstonia solanacearum:0.11464)100:0.08478)75:0.03840,Nitrosomonas europaea:0.22059)100:0.08761)100:0.16913,((((((Agrobacterium tumefaciens Cereon:0.00000,Agrobacterium tumefaciens WashU:0.00000)100:0.05735,Rhizobium meliloti:0.05114)100:0.05575,((Brucella suis:0.00102,Brucella melitensis:0.00184)100:0.08660,Rhizobium loti:0.09308)51:0.02384)100:0.08637,(Rhodopseudomonas palustris:0.04182,Bradyrhizobium japonicum:0.06346)100:0.14122)100:0.05767,Caulobacter crescentus:0.23943)100:0.11257,(Wolbachia sp. wMel:0.51596,(Rickettsia prowazekii:0.04245,Rickettsia conorii:0.02487)100:0.38019)100:0.12058)100:0.12365)100:0.06301,((((Helicobacter pylori J99:0.00897,Helicobacter pylori 26695:0.00637)100:0.19055,Helicobacter hepaticus:0.12643)100:0.05330,Wolinella succinogenes:0.11644)100:0.09105,Campylobacter jejuni:0.20399)100:0.41390)82:0.04428,((Desulfovibrio vulgaris:0.38320,(Geobacter sulfurreducens:0.22491,Bdellovibrio bacteriovorus:0.45934)43:0.04870)69:0.04100,(Acidobacterium capsulatum:0.24572,Solibacter usitatus:0.29086)100:0.20514)64:0.04214)98:0.05551,((Fusobacterium nucleatum:0.45615,(Aquifex aeolicus:0.40986,Thermotoga maritima:0.34182)100:0.07696)35:0.03606,(((Thermus thermophilus:0.26583,Deinococcus radiodurans:0.29763)100:0.24776,Dehalococcoides ethenogenes:0.53988)35:0.04370,((((Nostoc sp. PCC 7120:0.12014,Synechocystis sp. PCC6803:0.15652)98:0.04331,Synechococcus elongatus:0.13147)100:0.05040,(((Synechococcus sp. WH8102:0.06780,Prochlorococcus marinus MIT9313:0.05434)100:0.04879,Prochlorococcus marinus SS120:0.10211)74:0.04238,Prochlorococcus marinus CCMP1378:0.16170)100:0.20442)100:0.07646,Gloeobacter violaceus:0.23764)100:0.24501)39:0.04332)51:0.02720)74:0.03471,((((Gemmata obscuriglobus:0.36751,Rhodopirellula baltica:0.38017)100:0.24062,((Leptospira interrogans L1-130:0.00000,Leptospira interrogans 56601:0.00027)100:0.47573,((Treponema pallidum:0.25544,Treponema denticola:0.16072)100:0.19057,Borrelia burgdorferi:0.42323)100:0.20278)95:0.07248)42:0.04615,(((Tropheryma whipplei TW08/27:0.00009,Tropheryma whipplei Twist:0.00081)100:0.44723,Bifidobacterium longum:0.29283)100:0.14429,(((((Corynebacterium glutamicum 13032:0.00022,Corynebacterium glutamicum:0.00000)100:0.03415,Corynebacterium efficiens:0.02559)100:0.03682,Corynebacterium diphtheriae:0.06479)100:0.13907,(((Mycobacterium bovis:0.00067,(Mycobacterium tuberculosis CDC1551:0.00000,Mycobacterium tuberculosis H37Rv:0.00000)98:0.00022)100:0.03027,Mycobacterium leprae:0.05135)97:0.01514,Mycobacterium paratuberculosis:0.02091)100:0.11523)100:0.09883,(Streptomyces avermitilis:0.02680,Streptomyces coelicolor:0.02678)100:0.16707)91:0.06110)100:0.26800)23:0.03480,((Fibrobacter succinogenes:0.51984,(Chlorobium tepidum:0.37204,(Porphyromonas gingivalis:0.11304,Bacteroides thetaiotaomicron:0.13145)100:0.34694)100:0.09237)62:0.04841,(((Chlamydophila pneumoniae TW183:0.00000,(Chlamydia pneumoniae J138:0.00000,(Chlamydia pneumoniae CWL029:0.00000,Chlamydia pneumoniae AR39:0.00000)37:0.00000)44:0.00000)100:0.10482,Chlamydophila caviae:0.05903)98:0.04170,(Chlamydia muridarum:0.01938,Chlamydia trachomatis:0.02643)100:0.06809)100:0.60169)32:0.04443)67:0.04284)66:0.02646,((Thermoanaerobacter tengcongensis:0.17512,((Clostridium tetani:0.10918,Clostridium perfringens:0.11535)78:0.03238,Clostridium acetobutylicum:0.11396)100:0.15056)100:0.11788,(((((Mycoplasma mobile:0.27702,Mycoplasma pulmonis:0.28761)100:0.28466,((((Mycoplasma pneumoniae:0.10966,Mycoplasma genitalium:0.11268)100:0.31768,Mycoplasma gallisepticum:0.24373)100:0.14180,Mycoplasma penetrans:0.34890)94:0.06674,Ureaplasma parvum:0.33874)100:0.19177)100:0.07341,Mycoplasma mycoides:0.37680)100:0.12541,Phytoplasma Onion yellows:0.47843)100:0.09099,(((((Listeria monocytogenes F2365:0.00063,Listeria monocytogenes EGD:0.00144)90:0.00235,Listeria innocua:0.00248)100:0.13517,((Oceanobacillus iheyensis:0.13838,Bacillus halodurans:0.09280)91:0.02676,(((Bacillus cereus ATCC 14579:0.00342,Bacillus cereus ATCC 10987:0.00123)100:0.00573,Bacillus anthracis:0.00331)100:0.08924,Bacillus subtilis:0.07876)96:0.01984)100:0.03907)69:0.02816,((Staphylococcus aureus MW2:0.00000,(Staphylococcus aureus N315:0.00022,Staphylococcus aureus Mu50:0.00022)61:0.00022)100:0.02479,Staphylococcus epidermidis:0.03246)100:0.17366)64:0.02828,(((((((Streptococcus agalactiae III:0.00110,Streptococcus agalactiae V:0.00155)100:0.01637,(Streptococcus pyogenes M1:0.00134,(Streptococcus pyogenes MGAS8232:0.00045,(Streptococcus pyogenes MGAS315:0.00000,Streptococcus pyogenes SSI-1:0.00022)100:0.00110)87:0.00066)100:0.02250)100:0.01360,Streptococcus mutans:0.04319)99:0.01920,(Streptococcus pneumoniae R6:0.00119,Streptococcus pneumoniae TIGR4:0.00124)100:0.03607)100:0.04983,Lactococcus lactis:0.11214)100:0.08901,Enterococcus faecalis:0.07946)100:0.03958,(Lactobacillus johnsonii:0.20999,Lactobacillus plantarum:0.14371)100:0.06763)100:0.08989)100:0.08905)92:0.09540)54:0.04315)Bacteria:1.34959,(((((Thalassiosira pseudonana:0.33483,(Cryptosporidium hominis:0.25048,Plasmodium falciparum:0.28267)100:0.14359)42:0.03495,(((Oryza sativa:0.07623,Arabidopsis thaliana:0.09366)100:0.15770,Cyanidioschyzon merolae:0.38319)96:0.08133,(Dictyostelium discoideum:0.34685,(((Eremothecium gossypii:0.07298,Saccharomyces cerevisiae:0.07619)100:0.21170,Schizosaccharomyces pombe:0.24665)100:0.15370,(((Anopheles gambiae:0.10724,Drosophila melanogaster:0.10233)100:0.09870,((Takifugu rubripes:0.03142,Danio rerio:0.05230)100:0.04335,(((Rattus norvegicus:0.03107,Mus musculus:0.01651)91:0.00398,(Homo sapiens:0.00957,Pan troglodytes:0.03864)100:0.01549)99:0.01629,Gallus gallus:0.04596)100:0.01859)100:0.09688)95:0.03693,(Caenorhabditis elegans:0.01843,Caenorhabditis briggsae:0.01896)100:0.24324)100:0.09911)85:0.04004)41:0.02708)44:0.02636)87:0.06455,Leishmania major:0.45664)100:0.10129,Giardia lamblia:0.55482)100:0.57543,((Nanoarchaeum equitans:0.81078,(((Sulfolobus tokodaii:0.17389,Sulfolobus solfataricus:0.18962)100:0.33720,Aeropyrum pernix:0.43380)94:0.09462,Pyrobaculum aerophilum:0.55514)100:0.12018)100:0.15444,((Thermoplasma volcanium:0.10412,Thermoplasma acidophilum:0.09785)100:0.66151,((((Methanobacterium thermautotrophicum:0.36583,Methanopyrus kandleri:0.35331)99:0.07446,(Methanococcus maripaludis:0.28592,Methanococcus jannaschii:0.13226)100:0.23828)100:0.06284,((Pyrococcus horikoshii:0.02786,Pyrococcus abyssi:0.02179)100:0.02239,Pyrococcus furiosus:0.02366)100:0.36220)51:0.04469,(Archaeoglobus fulgidus:0.34660,(Halobacterium sp. NRC-1:0.61597,(Methanosarcina acetivorans:0.02602,Methanosarcina mazei:0.03087)100:0.30588)100:0.12801)100:0.10395)62:0.06815)99:0.11833)100:0.43325):0.88776);
    (((((((((((((((((((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:0.07619)Saccharomycetaceae:0.21170[100],Schizosaccharomyces_pombe:0.24665)Ascomycota:0.15370[100],(((Anopheles_gambiae:0.10724,Drosophila_melanogaster:0.10233)Diptera:0.09870[100],((Takifugu_rubripes:0.03142,Danio_rerio:0.05230)Actinopterygii:0.04335[100],(((Rattus_norvegicus:0.03107,Mus_musculus:0.01651)Murinae:0.00398[91],(Homo_sapiens:0.00957,Pan_troglodytes:0.03864)Hominidae:0.01549[100])Euarchontoglires:0.01629[99],Gallus_gallus:0.04596)Gnathostomata_subclade:0.01859[100])Gnathostomata:0.09688[100])Metazoa_subclade:0.03693[95],(Caenorhabditis_elegans:0.01843,Caenorhabditis_briggsae:0.01896)Caenorhabditis:0.24324[100])Metazoa:0.09911[100])Eukaryota_subclade:0.04004[85])Eukaryota_subclade:0.02708[41])Eukaryota_subclade:0.02636[44])Eukaryota_subclade:0.06455[87],Leishmania_major:0.45664)Eukaryota_subclade:0.10129[100],Giardia_lamblia:0.55482)Eukaryota:0.57543[100],((Nanoarchaeum_equitans:0.81078,(((Sulfolobus_tokodaii:0.17389,Sulfolobus_solfataricus:0.18962)Sulfolobus:0.33720[100],Aeropyrum_pernix:0.43380)Thermoprotei_subclade:0.09462[94],Pyrobaculum_aerophilum:0.55514)Thermoprotei:0.12018[100])Archaea_subclade:0.15444[100],((Thermoplasma_volcanium:0.10412,Thermoplasma_acidophilum:0.09785)Thermoplasma:0.66151[100],((((Methanobacterium_thermautotrophicum:0.36583,Methanopyrus_kandleri:0.35331)Euryarchaeota_subclade:0.07446[99],(Methanococcus_maripaludis:0.28592,Methanococcus_jannaschii:0.13226)Methanococcales:0.23828[100])Euryarchaeota_subclade:0.06284[100],((Pyrococcus_horikoshii:0.02786,Pyrococcus_abyssi:0.02179)Pyrococcus_subclade:0.02239[100],Pyrococcus_furiosus:0.02366)Pyrococcus:0.36220[100])Euryarchaeota_subclade:0.04469[51],(Archaeoglobus_fulgidus:0.34660,(Halobacterium_sp._NRC-1:0.61597,(Methanosarcina_acetivorans:0.02602,Methanosarcina_mazei:0.03087)Methanosarcina:0.30588[100])Euryarchaeota_subclade:0.12801[100])Euryarchaeota_subclade:0.10395[100])Euryarchaeota_subclade:0.06815[62])Euryarchaeota:0.11833[99])Archaea:0.43325[100]):0.88776);
  14. mbostock revised this gist Oct 19, 2015. 1 changed file with 2 additions and 2 deletions.
    4 changes: 2 additions & 2 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -51,7 +51,7 @@
    <script>

    var outerRadius = 960 / 2,
    innerRadius = outerRadius - 180;
    innerRadius = outerRadius - 170;

    var cluster = d3.layout.cluster()
    .size([360, innerRadius])
    @@ -95,7 +95,7 @@
    .enter().append("text")
    .attr("class", "label")
    .attr("dy", ".31em")
    .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 6) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
    .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
    .style("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
    .text(function(d) { return d.name; })
    .on("mouseover", mouseovered(true))
  15. mbostock revised this gist Oct 19, 2015. 1 changed file with 1 addition and 1 deletion.
    2 changes: 1 addition & 1 deletion index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -140,7 +140,7 @@
    c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI),
    s1 = Math.sin(endAngle);
    return "M" + startRadius * c0 + "," + startRadius * s0
    + (endAngle === startAngle ? "" : "A" + endRadius + "," + endRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
    + (endAngle === startAngle ? "" : "A" + startRadius + "," + startRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
    + "L" + endRadius * c1 + "," + endRadius * s1;
    }

  16. mbostock revised this gist Oct 19, 2015. 1 changed file with 9 additions and 5 deletions.
    14 changes: 9 additions & 5 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -76,21 +76,21 @@

    adjustDepth(root, 0);

    var linkExtension = svg.selectAll(".link-extension")
    var linkExtension = svg.append("g").selectAll(".link-extension")
    .data(links.filter(function(d) { return !d.target.children; }))
    .enter().append("path")
    .each(function(d) { d.target.linkExtensionNode = this; })
    .attr("class", "link-extension")
    .attr("d", function(d) { return step(d.target.x, d.target.y, d.target.x, innerRadius); });

    var link = svg.selectAll(".link")
    var link = svg.append("g").selectAll(".link")
    .data(links)
    .enter().append("path")
    .each(function(d) { d.target.linkNode = this; })
    .attr("class", "link")
    .attr("d", function(d) { return step(d.source.x, d.source.y, d.target.x, d.target.y) });

    svg.selectAll(".label")
    svg.append("g").selectAll(".label")
    .data(nodes.filter(function(d) { return !d.children; }))
    .enter().append("text")
    .attr("class", "label")
    @@ -113,10 +113,14 @@
    function mouseovered(active) {
    return function(d) {
    d3.select(this).classed("label--active", active);
    d3.select(d.linkExtensionNode).classed("link-extension--active", active);
    do d3.select(d.linkNode).classed("link--active", active); while (d = d.parent);
    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 depth of any node in the phylogenetic tree.
  17. mbostock revised this gist Oct 19, 2015. 1 changed file with 3 additions and 0 deletions.
    3 changes: 3 additions & 0 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -42,8 +42,11 @@
    <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 2015 Mike Bostock http://d3js.org -->
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js" charset="utf-8"></script>
    <script>

  18. mbostock revised this gist Oct 19, 2015. 1 changed file with 12 additions and 6 deletions.
    18 changes: 12 additions & 6 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -14,11 +14,6 @@
    stroke: #000;
    }

    .link--active {
    stroke: #f00;
    stroke-width: 1.5px;
    }

    .link-extension {
    fill: none;
    stroke: #000;
    @@ -29,8 +24,17 @@
    font: 10px sans-serif;
    }

    .link--active {
    stroke: #f00;
    stroke-width: 1.5px;
    }

    .link-extension--active {
    stroke: #f00;
    }

    .label--active {
    fill: red;
    fill: #f00;
    font-weight: bold;
    }

    @@ -72,6 +76,7 @@
    var linkExtension = svg.selectAll(".link-extension")
    .data(links.filter(function(d) { return !d.target.children; }))
    .enter().append("path")
    .each(function(d) { d.target.linkExtensionNode = this; })
    .attr("class", "link-extension")
    .attr("d", function(d) { return step(d.target.x, d.target.y, d.target.x, innerRadius); });

    @@ -105,6 +110,7 @@
    function mouseovered(active) {
    return function(d) {
    d3.select(this).classed("label--active", active);
    d3.select(d.linkExtensionNode).classed("link-extension--active", active);
    do d3.select(d.linkNode).classed("link--active", active); while (d = d.parent);
    };
    }
  19. mbostock created this gist Oct 19, 2015.
    3 changes: 3 additions & 0 deletions README.md
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,3 @@
    A re-implementation of Jason Davies’ [Phylogenetic Tree of Life](https://www.jasondavies.com/tree-of-life/), with faded gray lines to connect the leaf nodes of the tree to their corresponding labels inspired by [a figure from *Nature*](http://www.nature.com/nature/journal/v462/n7276/fig_tab/nature08656_F1.html).

    This implementation modifies the depth of interior nodes in a [cluster layout](https://github.com/mbostock/d3/wiki/Cluster-Layout) to show branch lengths. Toggle the checkbox in the top-left corner to show or hide branch lengths, and mouseover a label to highlight its path to the root.
    136 changes: 136 additions & 0 deletions index.html
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,136 @@
    <!DOCTYPE html>
    <meta charset="utf-8">
    <style>

    #show-length {
    font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
    position: absolute;
    top: 10px;
    left: 10px;
    }

    .link {
    fill: none;
    stroke: #000;
    }

    .link--active {
    stroke: #f00;
    stroke-width: 1.5px;
    }

    .link-extension {
    fill: none;
    stroke: #000;
    stroke-opacity: .25;
    }

    .label {
    font: 10px sans-serif;
    }

    .label--active {
    fill: red;
    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>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.min.js" charset="utf-8"></script>
    <script>

    var outerRadius = 960 / 2,
    innerRadius = outerRadius - 180;

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

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

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

    var root = parseNewick(life),
    nodes = cluster.nodes(root),
    links = cluster.links(nodes),
    scale = innerRadius / maxDepth(root),
    input = d3.select("#show-length input").on("change", changed),
    timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

    adjustDepth(root, 0);

    var linkExtension = svg.selectAll(".link-extension")
    .data(links.filter(function(d) { return !d.target.children; }))
    .enter().append("path")
    .attr("class", "link-extension")
    .attr("d", function(d) { return step(d.target.x, d.target.y, d.target.x, innerRadius); });

    var link = svg.selectAll(".link")
    .data(links)
    .enter().append("path")
    .each(function(d) { d.target.linkNode = this; })
    .attr("class", "link")
    .attr("d", function(d) { return step(d.source.x, d.source.y, d.target.x, d.target.y) });

    svg.selectAll(".label")
    .data(nodes.filter(function(d) { return !d.children; }))
    .enter().append("text")
    .attr("class", "label")
    .attr("dy", ".31em")
    .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 6) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
    .style("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
    .text(function(d) { return d.name; })
    .on("mouseover", mouseovered(true))
    .on("mouseout", mouseovered(false));

    function changed() {
    clearTimeout(timeout);
    var checked = this.checked;
    d3.transition().duration(750).each(function() {
    linkExtension.transition().attr("d", function(d) { return step(d.target.x, checked ? d.target.depth * scale : d.target.y, d.target.x, innerRadius); });
    link.transition().attr("d", function(d) { return step(d.source.x, checked ? d.source.depth * scale : d.source.y, d.target.x, checked ? d.target.depth * scale : d.target.y) });
    });
    }

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

    // Compute the maximum depth of any node in the phylogenetic tree.
    function maxDepth(d) {
    return (d.length || (d.length = 0)) + (d.children ? d3.max(d.children, maxDepth) : 0);
    }

    // Set the depth of each node by recursively summing the distance from the root.
    function adjustDepth(d, y0) {
    d.depth = y0 += d.length, d.children && d.children.forEach(function(d) { adjustDepth(d, y0); });
    }

    // Like d3.svg.diagonal.radial, but with square corners.
    function step(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" + endRadius + "," + endRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
    + "L" + endRadius * c1 + "," + endRadius * s1;
    }

    d3.select(self.frameElement).style("height", outerRadius * 2 + "px");

    </script>
    1 change: 1 addition & 0 deletions life.txt
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1 @@
    (((((((((((((((((((Escherichia coli EDL933:0.00000,Escherichia coli O157 H7:0.00000)96:0.00044,((Escherichia coli O6:0.00000,Escherichia coli K12:0.00022)76:0.00022,(Shigella flexneri 2a 2457T:0.00000,Shigella flexneri 2a 301:0.00000)100:0.00266)75:0.00000)100:0.00813,((Salmonella enterica:0.00000,Salmonella typhi:0.00000)100:0.00146,Salmonella typhimurium:0.00075)100:0.00702)100:0.03131,((Yersinia pestis Medievalis:0.00000,(Yersinia pestis KIM:0.00000,Yersinia pestis CO92:0.00000)31:0.00000)100:0.03398,Photorhabdus luminescens:0.05076)61:0.01182)98:0.02183,((Blochmannia floridanus:0.32481,Wigglesworthia brevipalpis:0.35452)100:0.08332,(Buchnera aphidicola Bp:0.27492,(Buchnera aphidicola APS:0.09535,Buchnera aphidicola Sg:0.10235)100:0.10140)100:0.06497)100:0.15030)100:0.02808,((Pasteurella multocida:0.03441,Haemophilus influenzae:0.03754)94:0.01571,Haemophilus ducreyi:0.05333)100:0.07365)100:0.03759,((((Vibrio vulnificus YJ016:0.00021,Vibrio vulnificus CMCP6:0.00291)100:0.01212,Vibrio parahaemolyticus:0.01985)100:0.01536,Vibrio cholerae:0.02995)100:0.02661,Photobacterium profundum:0.06131)100:0.05597)81:0.03492,Shewanella oneidensis:0.10577)100:0.12234,((Pseudomonas putida:0.02741,Pseudomonas syringae:0.03162)100:0.02904,Pseudomonas aeruginosa:0.03202)100:0.14456)98:0.04492,((Xylella fastidiosa 700964:0.01324,Xylella fastidiosa 9a5c:0.00802)100:0.10192,(Xanthomonas axonopodis:0.01069,Xanthomonas campestris:0.00934)100:0.05037)100:0.24151)49:0.02475,Coxiella burnetii:0.33185)54:0.03328,((((Neisseria meningitidis A:0.00400,Neisseria meningitidis B:0.00134)100:0.12615,Chromobacterium violaceum:0.09623)100:0.07131,((Bordetella pertussis:0.00127,(Bordetella parapertussis:0.00199,Bordetella bronchiseptica:0.00022)67:0.00006)100:0.14218,Ralstonia solanacearum:0.11464)100:0.08478)75:0.03840,Nitrosomonas europaea:0.22059)100:0.08761)100:0.16913,((((((Agrobacterium tumefaciens Cereon:0.00000,Agrobacterium tumefaciens WashU:0.00000)100:0.05735,Rhizobium meliloti:0.05114)100:0.05575,((Brucella suis:0.00102,Brucella melitensis:0.00184)100:0.08660,Rhizobium loti:0.09308)51:0.02384)100:0.08637,(Rhodopseudomonas palustris:0.04182,Bradyrhizobium japonicum:0.06346)100:0.14122)100:0.05767,Caulobacter crescentus:0.23943)100:0.11257,(Wolbachia sp. wMel:0.51596,(Rickettsia prowazekii:0.04245,Rickettsia conorii:0.02487)100:0.38019)100:0.12058)100:0.12365)100:0.06301,((((Helicobacter pylori J99:0.00897,Helicobacter pylori 26695:0.00637)100:0.19055,Helicobacter hepaticus:0.12643)100:0.05330,Wolinella succinogenes:0.11644)100:0.09105,Campylobacter jejuni:0.20399)100:0.41390)82:0.04428,((Desulfovibrio vulgaris:0.38320,(Geobacter sulfurreducens:0.22491,Bdellovibrio bacteriovorus:0.45934)43:0.04870)69:0.04100,(Acidobacterium capsulatum:0.24572,Solibacter usitatus:0.29086)100:0.20514)64:0.04214)98:0.05551,((Fusobacterium nucleatum:0.45615,(Aquifex aeolicus:0.40986,Thermotoga maritima:0.34182)100:0.07696)35:0.03606,(((Thermus thermophilus:0.26583,Deinococcus radiodurans:0.29763)100:0.24776,Dehalococcoides ethenogenes:0.53988)35:0.04370,((((Nostoc sp. PCC 7120:0.12014,Synechocystis sp. PCC6803:0.15652)98:0.04331,Synechococcus elongatus:0.13147)100:0.05040,(((Synechococcus sp. WH8102:0.06780,Prochlorococcus marinus MIT9313:0.05434)100:0.04879,Prochlorococcus marinus SS120:0.10211)74:0.04238,Prochlorococcus marinus CCMP1378:0.16170)100:0.20442)100:0.07646,Gloeobacter violaceus:0.23764)100:0.24501)39:0.04332)51:0.02720)74:0.03471,((((Gemmata obscuriglobus:0.36751,Rhodopirellula baltica:0.38017)100:0.24062,((Leptospira interrogans L1-130:0.00000,Leptospira interrogans 56601:0.00027)100:0.47573,((Treponema pallidum:0.25544,Treponema denticola:0.16072)100:0.19057,Borrelia burgdorferi:0.42323)100:0.20278)95:0.07248)42:0.04615,(((Tropheryma whipplei TW08/27:0.00009,Tropheryma whipplei Twist:0.00081)100:0.44723,Bifidobacterium longum:0.29283)100:0.14429,(((((Corynebacterium glutamicum 13032:0.00022,Corynebacterium glutamicum:0.00000)100:0.03415,Corynebacterium efficiens:0.02559)100:0.03682,Corynebacterium diphtheriae:0.06479)100:0.13907,(((Mycobacterium bovis:0.00067,(Mycobacterium tuberculosis CDC1551:0.00000,Mycobacterium tuberculosis H37Rv:0.00000)98:0.00022)100:0.03027,Mycobacterium leprae:0.05135)97:0.01514,Mycobacterium paratuberculosis:0.02091)100:0.11523)100:0.09883,(Streptomyces avermitilis:0.02680,Streptomyces coelicolor:0.02678)100:0.16707)91:0.06110)100:0.26800)23:0.03480,((Fibrobacter succinogenes:0.51984,(Chlorobium tepidum:0.37204,(Porphyromonas gingivalis:0.11304,Bacteroides thetaiotaomicron:0.13145)100:0.34694)100:0.09237)62:0.04841,(((Chlamydophila pneumoniae TW183:0.00000,(Chlamydia pneumoniae J138:0.00000,(Chlamydia pneumoniae CWL029:0.00000,Chlamydia pneumoniae AR39:0.00000)37:0.00000)44:0.00000)100:0.10482,Chlamydophila caviae:0.05903)98:0.04170,(Chlamydia muridarum:0.01938,Chlamydia trachomatis:0.02643)100:0.06809)100:0.60169)32:0.04443)67:0.04284)66:0.02646,((Thermoanaerobacter tengcongensis:0.17512,((Clostridium tetani:0.10918,Clostridium perfringens:0.11535)78:0.03238,Clostridium acetobutylicum:0.11396)100:0.15056)100:0.11788,(((((Mycoplasma mobile:0.27702,Mycoplasma pulmonis:0.28761)100:0.28466,((((Mycoplasma pneumoniae:0.10966,Mycoplasma genitalium:0.11268)100:0.31768,Mycoplasma gallisepticum:0.24373)100:0.14180,Mycoplasma penetrans:0.34890)94:0.06674,Ureaplasma parvum:0.33874)100:0.19177)100:0.07341,Mycoplasma mycoides:0.37680)100:0.12541,Phytoplasma Onion yellows:0.47843)100:0.09099,(((((Listeria monocytogenes F2365:0.00063,Listeria monocytogenes EGD:0.00144)90:0.00235,Listeria innocua:0.00248)100:0.13517,((Oceanobacillus iheyensis:0.13838,Bacillus halodurans:0.09280)91:0.02676,(((Bacillus cereus ATCC 14579:0.00342,Bacillus cereus ATCC 10987:0.00123)100:0.00573,Bacillus anthracis:0.00331)100:0.08924,Bacillus subtilis:0.07876)96:0.01984)100:0.03907)69:0.02816,((Staphylococcus aureus MW2:0.00000,(Staphylococcus aureus N315:0.00022,Staphylococcus aureus Mu50:0.00022)61:0.00022)100:0.02479,Staphylococcus epidermidis:0.03246)100:0.17366)64:0.02828,(((((((Streptococcus agalactiae III:0.00110,Streptococcus agalactiae V:0.00155)100:0.01637,(Streptococcus pyogenes M1:0.00134,(Streptococcus pyogenes MGAS8232:0.00045,(Streptococcus pyogenes MGAS315:0.00000,Streptococcus pyogenes SSI-1:0.00022)100:0.00110)87:0.00066)100:0.02250)100:0.01360,Streptococcus mutans:0.04319)99:0.01920,(Streptococcus pneumoniae R6:0.00119,Streptococcus pneumoniae TIGR4:0.00124)100:0.03607)100:0.04983,Lactococcus lactis:0.11214)100:0.08901,Enterococcus faecalis:0.07946)100:0.03958,(Lactobacillus johnsonii:0.20999,Lactobacillus plantarum:0.14371)100:0.06763)100:0.08989)100:0.08905)92:0.09540)54:0.04315)Bacteria:1.34959,(((((Thalassiosira pseudonana:0.33483,(Cryptosporidium hominis:0.25048,Plasmodium falciparum:0.28267)100:0.14359)42:0.03495,(((Oryza sativa:0.07623,Arabidopsis thaliana:0.09366)100:0.15770,Cyanidioschyzon merolae:0.38319)96:0.08133,(Dictyostelium discoideum:0.34685,(((Eremothecium gossypii:0.07298,Saccharomyces cerevisiae:0.07619)100:0.21170,Schizosaccharomyces pombe:0.24665)100:0.15370,(((Anopheles gambiae:0.10724,Drosophila melanogaster:0.10233)100:0.09870,((Takifugu rubripes:0.03142,Danio rerio:0.05230)100:0.04335,(((Rattus norvegicus:0.03107,Mus musculus:0.01651)91:0.00398,(Homo sapiens:0.00957,Pan troglodytes:0.03864)100:0.01549)99:0.01629,Gallus gallus:0.04596)100:0.01859)100:0.09688)95:0.03693,(Caenorhabditis elegans:0.01843,Caenorhabditis briggsae:0.01896)100:0.24324)100:0.09911)85:0.04004)41:0.02708)44:0.02636)87:0.06455,Leishmania major:0.45664)100:0.10129,Giardia lamblia:0.55482)100:0.57543,((Nanoarchaeum equitans:0.81078,(((Sulfolobus tokodaii:0.17389,Sulfolobus solfataricus:0.18962)100:0.33720,Aeropyrum pernix:0.43380)94:0.09462,Pyrobaculum aerophilum:0.55514)100:0.12018)100:0.15444,((Thermoplasma volcanium:0.10412,Thermoplasma acidophilum:0.09785)100:0.66151,((((Methanobacterium thermautotrophicum:0.36583,Methanopyrus kandleri:0.35331)99:0.07446,(Methanococcus maripaludis:0.28592,Methanococcus jannaschii:0.13226)100:0.23828)100:0.06284,((Pyrococcus horikoshii:0.02786,Pyrococcus abyssi:0.02179)100:0.02239,Pyrococcus furiosus:0.02366)100:0.36220)51:0.04469,(Archaeoglobus fulgidus:0.34660,(Halobacterium sp. NRC-1:0.61597,(Methanosarcina acetivorans:0.02602,Methanosarcina mazei:0.03087)100:0.30588)100:0.12801)100:0.10395)62:0.06815)99:0.11833)100:0.43325):0.88776);
    Binary file added thumbnail.png
    View file
    Loading
    Sorry, something went wrong. Reload?
    Sorry, we cannot display this file.
    Sorry, this file is invalid so it cannot be displayed.