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 caseP_{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