text: user180: I have a collection of phylogenetic trees produced from clustering DNA sequences, mostly a few nodes in each cluster/tree, with several clusters of size 1. And I would like to visualize them all together to get an idea of the relative sizes of the trees in the collection of clusters (cluster set).
  E.g.
  (ABC:0.0,('CL-118070':0.02010925,'CL-117615':0.00526463):0.00443474);
  (DEF:0.0,('CL-117360':0.00967856,'CL-117181':0.00967856):0.00990975);
  (GHI:0.0,('CL-123443':0.00123443,'CL-123443':0.00132446):0.00123435);
  (JKL:0.0,('CL-134123':0.00123441,'CL-545443':0.00343446):0.00134335);
  ((((CL-114948:0.00908659,(CL-114989:0.00324875,CL-114959:0.00536289):0.00037038):0.00457230,(CL-114851:0.01291841,CL-114831:0.00590321):0.00077034):0.03411459,XYZ:0.00251364):0.00207594,(CL-114950:0.03074481,CL-114699:0.02256162):0.00733986,CL-116426:0.01643848);
  
  I am thinking there must be a tool where I give it an input file with a tree per line and shows them as all in one go.
  Any suggestions:
  EDIT: looking at the options below:
  https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software
  FigTree: in this tool, one can load several trees, one per line, and there is a 'Prev/Next' menu to iterate over them, but no apparent option to display all of them at once.
  
  Phylo.io: in this tool, one can load several trees, and display one at a time or two of them, with colouring options that compare the common nodes/branches. There isn't an apparent option to visualize many trees in one go.
  
  PhyBin: this tool (https://cs.indiana.edu/~rrnewton/projects/phybin/) seems to cluster the sets of trees, but not visualize all of them together.
  GrapeTree: this tool () can visualize only one tree at a time. It displays the last tree in the list if more than one are copy+pasted in the input text box.
  
  There is another group of tools under Graph drawing:
  https://en.wikipedia.org/wiki/Graph_drawing
  Cytoscape: this tool is designed for network visualizations, which could be an option. Unsure if it visualizes newick trees, but there is are tools to convert trees to networks that could potentially work in combination with Cytoscape, e.g. https://github.com/MonsantoCo/Newick2Network
  
  user180: One possible solution is to use ETE Toolkit Treeview, which given a set of Newick files, it will show all of them, albeit connected as shown in the screenshot:
  
  
  user3381: I recommend using densitree: https://www.cs.auckland.ac.nz/~remco/DensiTree/
  And rwty: https://github.com/danlwarren/RWTY
  Densitree plots the superimposed set of trees in a heatmap-like format: 
  And rwty, a very powerful R package that allows visualisation of treespace in an NMDS format (among other methods): 
  
original_text: 180: <p>I have a collection of phylogenetic trees produced from clustering DNA sequences, mostly a few nodes in each cluster/tree, with several clusters of size 1. And I would like to visualize them all together to get an idea of the relative sizes of the trees in the collection of clusters (cluster set).</p>
  
  <p>E.g.</p>
  
  <pre><code>(ABC:0.0,('CL-118070':0.02010925,'CL-117615':0.00526463):0.00443474);
  (DEF:0.0,('CL-117360':0.00967856,'CL-117181':0.00967856):0.00990975);
  (GHI:0.0,('CL-123443':0.00123443,'CL-123443':0.00132446):0.00123435);
  (JKL:0.0,('CL-134123':0.00123441,'CL-545443':0.00343446):0.00134335);
  ((((CL-114948:0.00908659,(CL-114989:0.00324875,CL-114959:0.00536289):0.00037038):0.00457230,(CL-114851:0.01291841,CL-114831:0.00590321):0.00077034):0.03411459,XYZ:0.00251364):0.00207594,(CL-114950:0.03074481,CL-114699:0.02256162):0.00733986,CL-116426:0.01643848);
  </code></pre>
  
  <p>I am thinking there must be a tool where I give it an input file with a tree per line and shows them as all in one go.</p>
  
  <p>Any suggestions:</p>
  
  <p>EDIT: looking at the options below:</p>
  
  <p><a href="https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software</a></p>
  
  <p>FigTree: in this tool, one can load several trees, one per line, and there is a 'Prev/Next' menu to iterate over them, but no apparent option to display all of them at once.</p>
  
  <p><a href="https://i.stack.imgur.com/clNVV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/clNVV.png" alt="enter image description here"></a></p>
  
  <p>Phylo.io: in this tool, one can load several trees, and display one at a time or two of them, with colouring options that compare the common nodes/branches. There isn't an apparent option to visualize many trees in one go.</p>
  
  <p><a href="https://i.stack.imgur.com/bpObp.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/bpObp.png" alt="enter image description here"></a></p>
  
  <p>PhyBin: this tool (<a href="https://cs.indiana.edu/~rrnewton/projects/phybin/" rel="nofollow noreferrer">https://cs.indiana.edu/~rrnewton/projects/phybin/</a>) seems to cluster the sets of trees, but not visualize all of them together.</p>
  
  <p>GrapeTree: this tool () can visualize only one tree at a time. It displays the last tree in the list if more than one are copy+pasted in the input text box.</p>
  
  <p><a href="https://i.stack.imgur.com/JwjTw.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/JwjTw.png" alt="enter image description here"></a></p>
  
  <p>There is another group of tools under Graph drawing:
  <a href="https://en.wikipedia.org/wiki/Graph_drawing" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/Graph_drawing</a></p>
  
  <p>Cytoscape: this tool is designed for network visualizations, which could be an option. Unsure if it visualizes newick trees, but there is are tools to convert trees to networks that could potentially work in combination with Cytoscape, e.g. <a href="https://github.com/MonsantoCo/Newick2Network" rel="nofollow noreferrer">https://github.com/MonsantoCo/Newick2Network</a></p>
   180: <p>One possible solution is to use ETE Toolkit Treeview, which given a set of Newick files, it will show all of them, albeit connected as shown in the screenshot:</p>
  
  <p><a href="https://i.stack.imgur.com/6Ng17.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/6Ng17.png" alt="enter image description here"></a></p>
   3381: <p>I recommend using <code>densitree</code>: <a href="https://www.cs.auckland.ac.nz/~remco/DensiTree/" rel="nofollow noreferrer">https://www.cs.auckland.ac.nz/~remco/DensiTree/</a></p>
  
  <p>And <code>rwty</code>: <a href="https://github.com/danlwarren/RWTY" rel="nofollow noreferrer">https://github.com/danlwarren/RWTY</a></p>
  
  <p>Densitree plots the superimposed set of trees in a heatmap-like format: <a href="https://i.stack.imgur.com/6LcOe.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/6LcOe.jpg" alt="densitree"></a></p>
  
  <p>And <code>rwty</code>, a very powerful <code>R</code> package that allows visualisation of treespace in an NMDS format (among other methods): <a href="https://i.stack.imgur.com/S2fsR.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/S2fsR.png" alt="rwty"></a></p>
  