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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

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

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

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

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  • $\begingroup$ 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 $\endgroup$
    – M__ ♦
    Commented Nov 1, 2019 at 11:55
  • $\begingroup$ I suspect Rs ape can do the same thing but I'm not familiar with it $\endgroup$
    – M__ ♦
    Commented Nov 1, 2019 at 12:00
  • $\begingroup$ 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? $\endgroup$
    – terdon ♦
    Commented Nov 1, 2019 at 13:43
  • $\begingroup$ 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 $\endgroup$
    – Chris_Rands
    Commented Nov 1, 2019 at 15:01

4 Answers 4

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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

And rwty, a very powerful R package that allows visualisation of treespace in an NMDS format (among other methods): rwty

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    $\begingroup$ could you explain a little bit about both packages please? $\endgroup$
    – M__ ♦
    Commented Feb 25, 2020 at 12:27
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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

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  • $\begingroup$ If you think this is the answer, then we're good. I was thinking of printing unconnected trees on a single page $\endgroup$
    – M__ ♦
    Commented Nov 2, 2019 at 17:42
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For comparing a large number of trees side-by-side - Dendroscope.

For combining the trees into a network - Splitstree.

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Dendroscope is worth a look. I would also look into the R phangorn package.

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  • $\begingroup$ 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 $\endgroup$
    – M__ ♦
    Commented Nov 1, 2019 at 19:46

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