Phylogenetic Reconstruction

[gregcaporaso]

The latest content can be viewed here while in progress.

• background
  • why
  • how
• simulation code for asexual unicellular organism diverging over ~20 generations.
• challenges (different rates of evolution, homoplasy, HGT and other non-branching evolutionary changes).
• better example dataset (better real-world example of creating tree from biological sequences #11)
• distance-based approaches
  • some code and experiments in my sketchbook here
  • p versus d (JC-corrected) distances
  • upgma
  • wpgma (from SciPy)
• bootstrapping and jackknifing
• parsimony
• Bayesian
• maximum likelihood

Finally, a working with trees section, covering topics including:

• rooted versus unrooted trees
• rooting methods (e.g., page 21 of Phylogenetic Handbook)
  • midpoint
  • outgroup
• traversing trees
• filtering trees
• comparing trees, RFD etc.
• add tools section
  • MEGA and associated docs
  • FastTree and associated papers/docs

References:
https://www.ebi.ac.uk/training/online/course/introduction-phylogenetics
The Phylogenetic Handbook
http://evolution-textbook.org/content/free/contents/ch27.html