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. :-)

Vojtěch Zeisek

Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic

Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic

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