Lecture 3: A Brief Overview of Molecular Phylogeny - MCD Biology

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3. A bootstrap score >70% in a likelihood tree is pretty good; hold out for 80% with distance or
parsimony.
4. Note “jackknife” analysis: just like bootstrap, but you randomly throw away half the alignment
columns for each tree solution.
D. Check tree analysis with “signature sequences” (below).
8. Troubles you can get into with tree analysis (beyond bad sequence and bad alignment – big problems):
A. Rate differences in different lineages: Rapidly evolving lineages behave spuriously in trees.
e.g. with mitochondria: Actual tree: (rate-corrected)
Agrobacterium
Desulfovibrio Escherichia mitos