Answers.Body: <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.sstatic.net/6LcOe.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/S2fsR.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/S2fsR.png" alt="rwty"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-25T12:27:19.923Z
Answers.Text: could you explain a little bit about both packages please?
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-19T03:51:06.657Z
Answers.LastActivityDate: 2020-03-10T01:56:50.807Z
Answers.LastEditDate: 2020-03-10T01:56:50.807Z
Answers.UserDisplayName: user3479780
Answers.Body: <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.sstatic.net/6Ng17.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/6Ng17.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-02T17:42:02.393Z
Answers.Text: If you think this is the answer, then we're good. I was thinking of printing unconnected trees on a single page
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-01T15:05:05.800Z
Answers.LastActivityDate: 2019-11-01T15:05:05.800Z
Answers.UserDisplayName: 719016
Answers.Body: <p>For comparing a large number of trees side-by-side - Dendroscope.</p>
  
  <p>For combining the trees into a network - Splitstree.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-25T11:35:12.153Z
Answers.LastActivityDate: 2020-02-25T11:35:12.153Z
Answers.UserDisplayName: Laura
Answers.Body: <p>Dendroscope is worth a look.  I would also look into the R phangorn package.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-01T19:46:57.437Z
Answers.Text: Dendeoscope needs a hypothesis, and interpretation is hard (for the untrained eye). Consensus phylogeny is better. Ultimately we still don't know what the OP wants to achieve
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-01T18:06:36.743Z
Answers.LastActivityDate: 2019-11-01T18:06:36.743Z
Answers.UserDisplayName: Jay Moore
Body: <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.sstatic.net/clNVV.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/bpObp.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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.sstatic.net/JwjTw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-01T11:55:33.070Z
Comments.Text: The answer to the question is to do it programmatically via Pythons ETE and use Matplotlib graphing output options to produce multiple plots per diagram. The problem is we don't know how your tree files are stored. So I can put code but I'm not sure if you could modify for your purposes
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-01T12:00:31.463Z
Comments.Text: I suspect Rs ape can do the same thing but I'm not familiar with it
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-01T13:43:34.210Z
Comments.Text: How would they be displayed? Are you thinking of some sort of multi-tree alignment with the trees superimposed on top of one another? Or do you just want one next to the other?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-01T15:01:00.297Z
Comments.Text: What exactly are you trying to compare? You can just count the number of sequences in each cluster for starters. With a package like `ete3` you can count the number of leaves, number of nodes etc. in each tree. These kind of stats might be more informative than a visualisation depending on your interest
Comments.UserDisplayName: Chris_Rands
Tags: <phylogenetics><visualization><phylogeny>
Title: tool to visualize a collection of phylogenetic trees
ThreadText: # tool to visualize a collection of phylogenetic trees
  
  (Asked by: username_0 on 2019-11-01)
  
  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.
  
  [![enter image description here](https://i.sstatic.net/clNVV.png)](https://i.sstatic.net/clNVV.png)
  
  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.
  
  [![enter image description here](https://i.sstatic.net/bpObp.png)](https://i.sstatic.net/bpObp.png)
  
  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.
  
  [![enter image description here](https://i.sstatic.net/JwjTw.png)](https://i.sstatic.net/JwjTw.png)
  
  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>
  
  **Tags:** phylogenetics, visualization, phylogeny
  
  > **Comments:**
  > **username_1**: The answer to the question is to do it programmatically via Pythons ETE and use Matplotlib graphing output options to produce multiple plots per diagram. The problem is we don't know how your tree files are stored. So I can put code but I'm not sure if you could modify for your purposes  
  > **username_1**: I suspect Rs ape can do the same thing but I'm not familiar with it  
  > **username_2**: How would they be displayed? Are you thinking of some sort of multi-tree alignment with the trees superimposed on top of one another? Or do you just want one next to the other?  
  > **username_3**: What exactly are you trying to compare? You can just count the number of sequences in each cluster for starters. With a package like `ete3` you can count the number of leaves, number of nodes etc. in each tree. These kind of stats might be more informative than a visualisation depending on your interest  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_4 on 2020-02-19. Score: 2
  
  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: [![densitree](https://i.sstatic.net/6LcOe.jpg)](https://i.sstatic.net/6LcOe.jpg)
  
  And `rwty`, a very powerful `R` package that allows visualisation of treespace in an NMDS format (among other methods): [![rwty](https://i.sstatic.net/S2fsR.png)](https://i.sstatic.net/S2fsR.png)
  
  > **Comments:**
  > **username_1**: could you explain a little bit about both packages please?  
  
  ---
  
  ### Answer by username_0 on 2019-11-01. Score: 1
  
  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:
  
  [![enter image description here](https://i.sstatic.net/6Ng17.png)](https://i.sstatic.net/6Ng17.png)
  
  > **Comments:**
  > **username_1**: If you think this is the answer, then we're good. I was thinking of printing unconnected trees on a single page  
  
  ---
  
  ### Answer by username_5 on 2020-02-25. Score: 0
  
  For comparing a large number of trees side-by-side - Dendroscope.
  
  For combining the trees into a network - Splitstree.
  
  
  ---
  
  ### Answer by username_6 on 2019-11-01. Score: -1
  
  Dendroscope is worth a look. I would also look into the R phangorn package.
  
  > **Comments:**
  > **username_1**: Dendeoscope needs a hypothesis, and interpretation is hard (for the untrained eye). Consensus phylogeny is better. Ultimately we still don't know what the OP wants to achieve  
  
  ---
  
  