Computational Molecular Biology and Genomics 02-711/03-711/15-856Assignment 2: Phylogenomic Inference Due November 4th- Phylogenomics and the reconstruction of the tree of life. Delsuc F, Brinkmann, H. and Phillippe, H. Nat Rev Genet. May 2005; Vol 6, 361-365. Read this article and briefly answer the following questions. You may read additional materials, if you wish. If you do, you must cite your sources. You may not quote verbatim without attribution. 1. What is homoplasy? Why is homoplasy a problem?2. What are the two crucial steps of classical phylogenetic inference?3. Briefly explain the "supermatrix" and "supertree" methods. How are they similiar and how are they different? State one advantage of each approach.4. What are 'whole-genome features’? Explain the difference between sequence-basedmethods and methods based on whole-genome features.5. One method based on whole genome feature is the 'DNA string approach'.Briefly explain the principles. What are the pros and cons of this approach for tree reconstruction?6. What are rare genomic changes (RGCs)? What are the advantages of using RGCs inphylogeny reconstruction?7. What is horizontal gene transfer (HGT)? What is the effect of HGT on phylogeny reconstruction? 8. How is statistical consistentency for phylogenetic reconstruction method defined in this paper? Give three causes of inconsistency and explain each
View Full Document
Unlocking...