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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:

1. https://doi.org/10.7717/peerj.976

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

2. http://dx.doi.org/10.1016/j.meegid.2015.12.006

Highlight clades and annotate phylogenetic tree with genotype table.

3. http://dx.doi.org/10.3389%2Ffcimb.2016.00036

Annotate phylogenetic tree with binary matrix.

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

Annotate phylogenetic tree with sequence features.

5. http://dx.doi.org/10.1101/067207

Annotate with bootstrap values.

6. http://www.nature.com/articles/srep30158

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

7. http://dx.doi.org/10.1101/053371

8. http://dx.doi.org/10.1105/tpc.16.00053

9. http://dx.doi.org/10.1111/mec.13474

10. http://dx.doi.org/10.1371/journal.pone.0160958

11. http://dx.doi.org/10.1111/2041-210X.12593

12. http://dx.doi.org/10.1101/053371

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.