multiple alignments and phylogenies
play

Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark - PowerPoint PPT Presentation

Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark Voorhies Multiple Alignments and Phylogenies Review Computer lab notebook Dates Input/output/parameters Mark Voorhies Multiple Alignments and Phylogenies Review


  1. Multiple Alignments and Phylogenies Mark Voorhies 3/31/2011 Mark Voorhies Multiple Alignments and Phylogenies

  2. Review Computer “lab notebook” Dates Input/output/parameters Mark Voorhies Multiple Alignments and Phylogenies

  3. Review Computer “lab notebook” Dates Input/output/parameters (screenshots) Mark Voorhies Multiple Alignments and Phylogenies

  4. Review Computer “lab notebook” Dates Input/output/parameters (screenshots) E-mail result synopses ( e.g. , to PI) Mark Voorhies Multiple Alignments and Phylogenies

  5. Review Computer “lab notebook” Dates Input/output/parameters (screenshots) E-mail result synopses ( e.g. , to PI) BLAST Fast, heuristic local alignment with statistical foundation Mark Voorhies Multiple Alignments and Phylogenies

  6. Review Computer “lab notebook” Dates Input/output/parameters (screenshots) E-mail result synopses ( e.g. , to PI) BLAST Fast, heuristic local alignment with statistical foundation Gosh, we should have saved our BLAST reports! Mark Voorhies Multiple Alignments and Phylogenies

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

  8. 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

  9. 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

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

  11. 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

  12. 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

  13. Nomenclature Mark Voorhies Multiple Alignments and Phylogenies

  14. Nomenclature Mark Voorhies Multiple Alignments and Phylogenies

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Download Presentation
Download Policy: The content available on the website is offered to you 'AS IS' for your personal information and use only. It cannot be commercialized, licensed, or distributed on other websites without prior consent from the author. To download a presentation, simply click this link. If you encounter any difficulties during the download process, it's possible that the publisher has removed the file from their server.

Recommend


More recommend