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Today ggtree received 100 stars on and I found the paper was online at the same day by the tweet:
ggtree, Methods in Ecology and Evolutionに掲載されたのか。オープンアクセスっぽいな。https://t.co/JlET18BSZv
— ホクソピペット (@siero5335) August 16, 2016
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.
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