Inferring Evolutionary Relationships from Sequencing Data


  1. Research cladistics and phylogeny at Bozeman Science.  Review common misconceptions here.
  2. Select a virus to research. 
    NCBI is a free data repository (one of many) where people upload their sequenced data. They also have to include information called metadata which includes things like the location, date, species, sequencing method etc. associated with the sequence.  The Virus Variation Resource is a tool to easily search metadata and access virus sequences of interest.  
  3. Consider what types of samples you might be interested in, and what characteristics would allow you to highlight relationships between virus strains.
    If you are interested in a higher level of challenge, you may consider sequences of proteins extracted from yeast or bacterial pathogens.  
  4. Download sequence files of interest.
  5. Open SeaView and load your downloaded sequences.
  6. Make an alignement. An alignment does the best job at figuring out how the protein likely evolved and arranges the characters to reflect this.

  7. Once you have aligned your sequences you will build a tree from them! In the trees menu click PhyML, then click run on the menu that pops up.
  8. Once you have your tree click save as unrooted tree
  9. Trees are difficult to interpret so when presenting them its often advisable to use some color to make your data easier for the audience to digest.
  10. Load unrooted tree in Fig Tree and apply color based on information from metadata to highlight patterns.

  11. Submit your colorized tree, along with a one page executive summary identifying your pathogen of interest, describing the source of your data, and explaining molecular relationships you can infer from your tree.

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