I've just posted revised notes on Nested Clade Analysis. I haven't changed anything. I've only added a description of how to produce the “nested” set of haplotypes that are used for the next phase of the analysis. You'll find the new material at the beginning of the section entitled “Nested clade analysis”
I've also posted links to three papers (two on NCA, one on statistical phylogeography) that you may find interesting/useful.
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