multiple alignments and phylogenies
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Multiple Alignments and Phylogenies Mark Voorhies 3/29/2012 Mark - PowerPoint PPT Presentation

Multiple Alignments and Phylogenies Mark Voorhies 3/29/2012 Mark Voorhies Multiple Alignments and Phylogenies Comprehending our BLAST results We have a bunch of sequences that look similar to our query Mark Voorhies Multiple Alignments and


  1. Multiple Alignments and Phylogenies Mark Voorhies 3/29/2012 Mark Voorhies Multiple Alignments and Phylogenies

  2. Comprehending our BLAST results We have a bunch of sequences that look similar to our query Mark Voorhies Multiple Alignments and Phylogenies

  3. Comprehending our BLAST results We have a bunch of sequences that look similar to our query We infer that they are homologous to each other Mark Voorhies Multiple Alignments and Phylogenies

  4. Comprehending our BLAST results We have a bunch of sequences that look similar to our query We infer that they are homologous to each other What does that mean, anyway? Mark Voorhies Multiple Alignments and Phylogenies

  5. Nomenclature Homologs heritable elements with a common evolutionary origin. Mark Voorhies Multiple Alignments and Phylogenies

  6. Nomenclature Homologs heritable elements with a common evolutionary origin. Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome. Mark Voorhies Multiple Alignments and Phylogenies

  7. Nomenclature Homologs heritable elements with a common evolutionary origin. Orthologs homologs arising from speciation. Paralogs homologs arising from duplication and divergence within a single genome. Xenologs homologs arising from horizontal transfer. Onologs homologs arising from whole genome duplication. Mark Voorhies Multiple Alignments and Phylogenies

  8. Nomenclature Mark Voorhies Multiple Alignments and Phylogenies

  9. Nomenclature Mark Voorhies Multiple Alignments and Phylogenies

  10. Generating a multiple alignment in CLUSTALX Mark Voorhies Multiple Alignments and Phylogenies

  11. Generating a multiple alignment in CLUSTALX Mark Voorhies Multiple Alignments and Phylogenies

  12. Evolution implies a self-consistent model Distances Topology (Pairwise relationships) (Evolutionary history) Mark Voorhies Multiple Alignments and Phylogenies

  13. Measure all pairwise distances by dynamic programming Mark Voorhies Multiple Alignments and Phylogenies

  14. Measure all pairwise distances by dynamic programming Mark Voorhies Multiple Alignments and Phylogenies

  15. Generate a guide tree by UPGMA Mark Voorhies Multiple Alignments and Phylogenies

  16. Generate a guide tree by UPGMA Mark Voorhies Multiple Alignments and Phylogenies

  17. Generate a guide tree by UPGMA Mark Voorhies Multiple Alignments and Phylogenies

  18. Generate a guide tree by UPGMA Mark Voorhies Multiple Alignments and Phylogenies

  19. Generate a guide tree by UPGMA Mark Voorhies Multiple Alignments and Phylogenies

  20. Progressive alignment following the guide tree Mark Voorhies Multiple Alignments and Phylogenies

  21. Progressive alignment following the guide tree Mark Voorhies Multiple Alignments and Phylogenies

  22. Progressive alignment following the guide tree Mark Voorhies Multiple Alignments and Phylogenies

  23. Measure distances directly from the alignment Mark Voorhies Multiple Alignments and Phylogenies

  24. Generate neighbor-joining tree from new distances Mark Voorhies Multiple Alignments and Phylogenies

  25. Generate neighbor-joining tree from new distances Mark Voorhies Multiple Alignments and Phylogenies

  26. Generate neighbor-joining tree from new distances Mark Voorhies Multiple Alignments and Phylogenies

  27. Generate bootstrap values from subsets of the alignment Mark Voorhies Multiple Alignments and Phylogenies

  28. Generating a neighbor joining tree in CLUSTALX Mark Voorhies Multiple Alignments and Phylogenies

  29. Viewing the alignment and tree in JALVIEW Mark Voorhies Multiple Alignments and Phylogenies

  30. Related tools Multiple Alignment T-Coffee MUSCLE COBALT Tree building MrBayes (Bayesian MCMC) PhyML (maximum likelihood) Work benches MESQUITE UGENE Mark Voorhies Multiple Alignments and Phylogenies

  31. Searching with PSI-BLAST Mark Voorhies Multiple Alignments and Phylogenies

  32. Homework Play with CLUSTALX, JALVIEW, and PSI-BLAST Read PLoS Comp. Biol. 4:e1000069 Mark Voorhies Multiple Alignments and Phylogenies

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