[R-sig-phylo] Nucleotide diversity - different definitions and algorithms: pegas vs Arlequin

Good day all, The estimate of nucleotide diversity vary hugely between pegas and Arlequin, yet they both cite Nei (1987). For example, Arlequin = 0.7158 pegas = 0.003926426 With the same dataset. Their definitions of nucleotide diversity are also very different: Arlequin: It is computed

Re: [R-sig-phylo] Nucleotide diversity - different definitions and algorithms: pegas vs Arlequin

Hi Alastair, Alastair Potts wrote on 01/08/2011 14:19: Good day all, The estimate of nucleotide diversity vary hugely between pegas and Arlequin, yet they both cite Nei (1987). For example, Arlequin = 0.7158 pegas = 0.003926426 With the same dataset. Their definitions of nucleotide

Re: [R-sig-phylo] Nucleotide diversity - different definitions and algorithms: pegas vs Arlequin

Hi Emmanuel, Thanks for function. However, the problem actually lies with my misunderstanding of the the Arlequin output - I was mistaking the gene diversity result with nucleotide diversity (nucleotide diversity is the gene diversity divided by L loci). Both of your functions produce very