BSC4933(05)/ISC5224(01) Lab Report #8



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BSC4933(05)/ISC5224(01) Introduction to Bioinformatics Laboratory

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Lab Report #8

1) Which phylogenetic inference program and model seemed to give the most 'satisfying' answer? By this I mean, which method's results seemed most consistent with your preconceived notion of what the phylogeny should be, based on your sequences' descriptions. I don't need any quantification, just your 'gut' feeling. Choose only one from among all the methods used: GCG's Distances/GrowTree with either Kimura or Jukes-Cantor protein models; or GCG's PAUPSearch/PAUPDisplay with protein parsimony versus minimum evolution mean distance model; or any of the PHYLIP programs used, ProtDist/Fitch with the JTT model, bootstrapped neighbor-joining also with JTT, or ProtPars. Why might the method you chose here have given you your best answer?

2) What major problem seemed common to all of the inference methods using protein alignment data as a starting point in this tutorial? Describe this problem, why it occurs, where it comes from, how to deal with it.

3) Why should you use multiple, randomly-ordered runs, each with global tree rearrangements in heuristic phylogenetic inference, regardless of the method?

4) Did you designate an outgroup and what was it? Why did you chose that particular sequence?

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