ggtree paper published

August 16, 2016

(This article was first published on R on Guangchuang YU, and kindly contributed to R-bloggers)

Today ggtree received 100 stars on and I found the paper was online at the same day by the tweet:

I am quite exciting about it. Now ggtree is citable by doi:10.1111/2041-210X.12628.

In the review period, ggtree had already been cited by several papers:


Annotating phylogenetic tree with image files (i.e. secondary structure).


Highlight clades and annotate phylogenetic tree with genotype table.


Annotate phylogenetic tree with binary matrix.

4. http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00359

Annotate phylogenetic tree with sequence features.


Annotate with bootstrap values.


Visualize bootstrap value infer by RAxML and phyml on the same tree.







The ggtree paper provides several comprehensive and reproducible examples. It can be a good reference for complex tree annotation. My slides in 9th China R conference summarized the functionalities that ggtree provided.

More information can be found in ggtree homepage. Hope you have fun with ggtree.

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