Introduction to Phylogenetics
0.0.2
  • Reasons for making a phylogenetic tree
  • Phylogenetic pipeline
  • Building a tree in one click
  • Obtaining sequences
  • Aligning your sequences
  • Editing the alignment with Aliview
  • Introduction to distance methods
  • Building trees
  • Phylogenetic Course: Exercises
  • Slides and example files
  • Links
  • References
  • Glossary
Introduction to Phylogenetics
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Introduction to Phylogenetics¶

Contents¶

  • Reasons for making a phylogenetic tree
    • Molecular phylogenetics
  • Phylogenetic pipeline
  • Building a tree in one click
  • Obtaining sequences
    • Orthologues vs. paralogues
    • DNA or protein ?
  • Aligning your sequences
    • Methods
      • Progressive sequence alignment
      • Iterative methods
    • Multi-domains proteins
    • Low-complexity regions
  • Editing the alignment with Aliview
    • Introduction
      • Start aliview
      • Exercises
  • Introduction to distance methods
    • Constructing a phylogenetic tree of primates
      • Introduction
      • Exercise
      • Completed tables from exercise
      • Questions
      • Answers
    • Distance correction methods
  • Building trees
    • Introduction
    • File formats
  • Phylogenetic Course: Exercises
    • 1. Distance Based Method
    • 2. Parsimony Tree
    • 3. Calculating Maximum Likelihood Trees with RAxML
    • Calculating Bootstrapping Values with RAxML
    • Make ML tree from 10 runs starting with a different parsimony tree
      • Making 5 ML trees each starting from a different parsimonious tree will make max 10 runs on each
    • Drawing Bootstrap trees
    • Tree manipulations
    • Reference and Acknowledgements
    • Further Exercises
      • We pick a workflow name from the list of many from ete3 website and run it:
  • Slides and example files
    • Presentation slides
    • Example files
  • Links
  • References
    • Reading / Hands-on
    • Software
      • Multiple Alignment and Editing
      • Tree visualisation
  • Glossary
    • Homology
    • Homoplasy
    • Monophyly
    • Paraphyly
    • Polyphyly
    • Orthologs
    • Paralogs
    • In-paralogs
    • Out-paralogs
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© Copyright 2018, Marielle Vigouroux.

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