Melvin's digital garden

Reconstructing Ancestral Genomes

CREATED: 200709240333 ** Reconstruction accuracy analysis

  • focus on Fitch parsimony method in Jukes-Cantor evolutionary model
  • reconstruction accuracy ** unambiguous case P_{Acc1} = P_A({1}|1) = P_A({0}|0) ** ambiguous case P_{Acc2} = P_A({1}|1) + 1/2 P_A({0,1}|1) ** can be computed recursively by separating into cases ** depends on tree structure and conservation rate ** More genomes not necessarily better for reconstruction
  • More genomes more noise! ** Greedy algorithms for genome selection
  • Forward: add genomes one at a time
  • Backward: start with all genomes, remove one at a time ** Validation

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