Hi Vojtěch.

This kind of plot is possible to make using plotTree in phytools via the arguments tips (which sets the vertical coordinates of the tips, regardless of topology) & add (a logical value indicating whether to add the tree tree to an existing plot or to open a new plot). (All arguments for plotTree are documented in the man page for plotSimmap which plotTree uses internally.) Unfortunately, there is some complication. For instance, unless we set xlim & ylim, then plotTree will reset these values for each new plotted tree.

Later this evening I will do my best to make an example & post it to my blog.

- Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org

On 4/25/2017 12:20 PM, Vojtěch Zeisek wrote:
Hello,
for comparison of two trees I can use very nice function cophyloplot plotting
two trees (left and right) and connecting respective nodes by lines. Very nice
and convenient to read. But only for two trees. Displaying multiple trees in
multiple comparisons is not very convenient.
To display dozens to hundreds of trees there is densitree. Also nice, but for
this purpose I don't like its display.
I have several trees (~5) and I wish to compare their topologies, show
supports (at least for differing nodes) and highlight differences. I thought
about some overlay/parallel plotting (similar to the attached image) where
there would be complete topologies displayed and incongruences would be easily
visible. It would be probably doable by plotting all separate trees by
plot.phylo and then combining and tuning the figure in some vector editor
(like Inkscape). But I hope there is some more automated way to do it. :-)
Sincerely,
V.



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