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  1. http://evolution.genetics.washington.edu/phylip/newick_doc.html↩︎

  2. http://www.genetics.wustl.edu/eddy/forester/NHX.html↩︎

  3. https://sites.google.com/site/cmzmasek/home/software/archaeopteryx↩︎

  4. http://biopython.org/wiki/PAML↩︎

  5. http://bioperl.org/howtos/PAML_HOWTO.html↩︎

  6. https://github.com/ropensci/software-review/issues/179#issuecomment-369164110↩︎

  7. users can also use read.tree and read.nexus from ape to import phylogenetic tree from newick string and NEXUS file↩︎

  8. https://groups.google.com/forum/#!msg/bioc-ggtree/Q4LnwoTf1DM/uqYdYB_VBAAJ↩︎

  9. http://beast.community/nexus_metacomments↩︎

  10. http://beast.community/figtree↩︎

  11. http://tree.bio.ed.ac.uk/software/figtree/↩︎

  12. http://www.cbs.dtu.dk/services/NetNGlyc/↩︎

  13. If you want to plot the tree above the highlighting area, visit FAQ for details.↩︎

  14. https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree↩︎

  15. see also discussion in https://github.com/GuangchuangYu/ggtree/issues/78 and https://groups.google.com/d/msg/bioc-ggtree/VQqbF79NAWU/IjIvpQOBGwAJ↩︎

  16. the implementation was inspired by https://thackl.github.io/ggtree-composite-plots↩︎

  17. https://twitter.com/guangchuangyu/status/593443854541434882↩︎

  18. https://twitter.com/guangchuangyu/status/662095056610811904 and https://twitter.com/guangchuangyu/status/667337429704011777↩︎

  19. Google Noto emoji fonts was installed in my system↩︎

  20. the implementation was inspired by https://thackl.github.io/ggtree-composite-plots↩︎

  21. https://guangchuangyu.github.io/2016/07/how-to-bug-author/↩︎

  22. https://groups.google.com/d/msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ and https://github.com/GuangchuangYu/ggtree/issues/106↩︎

  23. https://twitter.com/hadleywickham/status/600280284869697538↩︎

  24. https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html↩︎

  25. https://groups.google.com/d/msg/bioc-ggtree/gruC4FztU8I/mwavqWCXAQAJ, https://groups.google.com/d/msg/bioc-ggtree/UoGQekWHIvw/ZswUUZKSGwAJ and https://github.com/GuangchuangYu/ggtree/issues/95↩︎

  26. example from: https://groups.google.com/d/msg/bioc-ggtree/T2ySvqv351g/mHsyljvBCwAJ↩︎