Compare topologies of trees with non-identical tip labels
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3.4 years ago
al-ash ▴ 170

I was using tanglegram() function from a great R package dendextend to draw comparison of phylogenetic trees. However, it requires to have identical set of tip labels in both trees and gives following error when presented with two trees with not identical set of tip labels:

Error in match_order_by_labels(dend2, dend1) : 
labels do not match in both trees.  Please make sure to fix the labels names!)

I have some trees where e.g. 80% of tip labels overlap but there are some tree-specific tips (e.g. one tree with tip labels A, B, C, D, E, F and another tree with labels C, D, E, F, G, H) which I'd love to compare.

Is there an existing tool to draw such a tree comparison (similar to the one produced by tanglegram: https://cran.r-project.org/web/packages/dendextend/vignettes/Cluster_Analysis.html)? Ideally R but I will be thankful for any platform. Thanks!

R dendextend tanglegram tree topology • 1.5k views
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Entering edit mode
3.4 years ago
jhc ★ 3.0k

you could try ete-compare to get some distances: http://etetoolkit.org/documentation/ete-compare/

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