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Session 6 - Wrap up the bioinformatics project

Introduction / Background information to session 6

This is the last session of the bioinformatics project (and of the course). You will wrap up the project and present your results to the class on March 6. The first 4-hour session will be used to prepare for the presentation.

Goals

  • Further your understanding of your results
  • Plot trees with a visualization software
  • Answer the question you were given in Session 2

Input(s)

  • The alignment for the mitochondria from session 3/5
  • The trees generated in Sessions 5

Output(s)

  • Image files of your trees
  • Slides for the presentation

Details

Reflect on your results

By now you have assembled a dataset to answer the question from Session 2; you collected cytB sequences and entire mitochondrial genomes for all species in the dataset; you aligned the species; you performed phylogenetic analysis and looked at some aspects of it, for example the model chosen; and you obtained a visual representation of your rooted trees.

Now it is time to reflect on all that you have done and to answer your phylogenetic question. The preferred method for that is to do it orally during Session 6. If for some reason this is not feasible, you will have to do it in a written form (details for the format are below).

At this stage, you should have two sets of trees: one for cytB and one for the entire mitochondria. To prepare for the presentation, think about:

  • What is the answer to the question given by these trees?

  • Do the different trees give the same answer? If not, what could be the explanation?

  • Which tree(s) do you think are most supported? What does the bootstrap analysis tell?

  • Are the substitution models different for cytB and the entire mitochondria? If yes, what could be an explanation?

  • Do you think your choice of species (including the outgroup) was appropriate to answer the question? If you were to redo the analysis, would you change something?

Upload your slides to Studium before 10 am on March 6 so we can download them to the computer that will be used for the presentations.

Presentation

On March 6th, we will meet in a lecture hall instead of the computer room. Each group will give a 5-10 minutes presentation about their project, presented with slides. The presentation should include (but is not limited to):

  • Introduce your question to the rest of the class
  • Briefly summarize the data you collected
  • Show your trees
  • Answer the main question of your project
  • Explain the outcome of your reflections (see questions above)

Back-up submission: Written report

In case you could not finish in time or if you are unable to present on March 6th, please let the teaching assistants know and submit a written document with your trees and 15-30 lines (or more if you are inspired) answering the questions through Studium. Do not forget to indicate which question you worked with and which species were included in the dataset. Exceptionally one submission by group is allowed - but remember to state the people involved.

END OF LABS, PLEASE READ THIS PART

This is the end of the lab, please make sure that you completed and wrote down the answers to all of the questions. Also, make sure to delete any files that you no longer need - you can copy them somewhere else if you want to keep them.

Obs! As this is the last session, this step is extra important. We won't delete anything before the end of the semester, but afterwards we do not guarantee that the data will be kept.