Lecture 17

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Phylogenetic Analysis

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Usually, analysis of confidence implies a "bootstrapping" procedure: rerun the analysis many times with partial data and analyze which features of the tree (branching order -> topology!) are well conserved, and which ones depend critically on unreliable features of the input data.

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Note that distance methods first reduce the explicit molecular data into a matrix of pairwise distances, then operate on that "summary" to construct the most plausible tree. They are fast, but less accurate than some alternatives.

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Genomes are and always have been exquisitly plastic, malleable entities. That we have long thought this not to be the case is a consequence of our limited personal experience and anthropocentric world view.

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