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Molecular Systematics & Evolution of Microorganisms

Distance Methods

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Table of Contents

  1. Distance Methods
  2. Some common models of sequence evolution used in distance analysis:
  3. Jukes and Cantor Model
  4. The Natural Logarithm is used to correct for superimposed changes at the same site
  5. A four taxon problem for Deinococcus and Thermus (Thermus, Deinococcus, Bacillus, Aquifex)
  6. Comparison of P distances and JC distances
  7. The 16S rRNA genes of Aquifex, Bacillus, Deinococcus and Thermus
  8. Distance models can be made more parameter rich to increase their realism 1
  9. Distance models can be made more parameter rich to increase their realism 2
  10. The logDet/paralinear distances method
  11. LogDet / Paralinear distances method
  12. LogDet - a worked example for two sequences A and B
  13. The logDet/paralinear distances method can find the true tree for Deinococcus + Thermus
  14. The logDet/paralinear distances method: advantages
  15. Distances: advantages:
  16. Distances: disadvantages:
  17. Site-Rate Heterogeneity can be a big Problem for Phylogenetic Analysis 1
  18. Site-Rate Heterogeneity can be a big Problem for Phylogenetic Analysis 2
  19. What is the First Branch in the Eukaryote Tree? - Microsporidia?
  20. Microsporidia have a number of unusual features
  21. Alternative explanations of Microsporidia unusual features
  22. Some inventions in eukaryote evolution?
  23. Maximum likelihood protein tree for Elongation factor 2
  24. One can reduce site-rate heterogeneity by editing data or including a site rate correction
  25. ML tree for EF-2 sequences in the absence of outgroups and with fast-evolving sites removed
  26. LogDet tree from variable sites (DNA, positions 1+2) for EF-2
  27. Effect of CSR and outgroup choice on Bootstrap support in LogDet analyses of EF-2 (DNA, positions 1+2)
  28. Some inventions in eukaryote evolution?
  29. Summary - Microsporidia are related to fungi
  30. Obtaining a tree using pairwise distances
  31. Obtaining a tree using pairwise distances
  32. An perfectly additive tree
  33. Obtaining a tree using pairwise distances
  34. Distance estimates may not make an additive tree
  35. Numbers of possible trees for N taxa:
  36. Obtaining a tree using pairwise distances
  37. Fitch Margoliash Method 1968:
  38. Fitch Margoliash Method 1968: an example
  39. Minimum Evolution method: an example
Author: Martin Embley 

Email: tme@nhm.ac.uk

Home Page: http://www.nhm.ac.uk/zoology/home/embley.htm