Phylogenetic Tree Computation Tutorial

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15/6/02Frank Olken - PGA PhylogenyTutorial1Phylogenetic TreeComputation TutorialFrank OlkenLawrence Berkeley National LabPresentation to PGA CourseMay 3, 2002Berkeley, California5/6/02Frank Olken - PGA PhylogenyTutorial2Overview Introduction: What? Why? ... Multiple Sequence Alignment Computing Phylogenetic Trees Merging Trees Resources Funding Sources25/6/02Frank Olken - PGA PhylogenyTutorial3Introduction5/6/02Fran k Olken - PGA PhylogenyTutorial4Example Seq. A = A A C C G G T T Seq. B = A A C C G G T G Seq. C = A C C C G G T C Seq. D = A C C C G G T AABCDABCDUnrootedTreeRootedTree35/6/02Fr ank Olken - PGA PhylogenyTutorial5Similarity vs. Homology Similar sequences resemble one another Homolog sequences derived from common ancestor Ortholog homologous sequences within a species Paralog homologous sequences between species5/6/02Frank Olken - PGA PhylogenyTutorial6Ortholog vs. Paralog Ortholog genomic variation occurs afterspeciation hence can be used forphylogeny of organism Paralog genetic duplication occurs beforespeciation hence not suitable forphylogeny of organism45/6/02Frank Olken - PGA PhylogenyTutorial7Homoplasy Sequence similarity NOT due to commonancestry May arise due to parallelism or convergentevolution Parallelism Convergent evolution5/6/02Frank Olken - PGA PhylogenyTutorial8Phylogenetic tree Binary tree ( , fan-out from nodes = 2) Variously rooted or unrooted tree topology Branch lengths (evolutionary time)55/6/02Frank Olken - P

1 5/6/02 Frank Olken - PGA Phylogeny Tutorial 1 Phylogenetic Tree Computation Tutorial Frank Olken Lawrence Berkeley National Lab Presentation to PGA Course

  Presentation, Tree, Tutorials, Computation, Phylogenetic tree computation tutorial, Phylogenetic