EZpopstat Instructions
EZpopstat computes standard population genetics statistics from an aligned FASTA file:
- Haplotype diversity (H), segregating sites (S), nucleotide diversity (π) and Tajima's D. Metrics are computed per population using per-population complete deletion. Standard deviations are reported for H and π.
- Pairwise FST. Hudson (1992) estimator elaborated by Bhatia et al. (2013). Requires a population map.
- AMOVA. One-level by default; upgrades to two-level hierarchical AMOVA (ΦCT, ΦSC, ΦST) when a group map is also provided. It uses global complete deletion and raw Hamming distances as in Excoffier et al. (1992). P-values are computed by label permutation
9999(more precise - recommended);999(faster);None(fastest but not recommended). Requires a population map. - Haplotype collapsing. It outputs a FASTA of unique haplotypes with frequency and population annotations.
- Aligned FASTA. All sequences must be aligned (
.fasta, .fa, .fna) - Population map (optional). Tab-separated, two columns:
ind001 PopA ind002 PopA ind003 PopB ind004 PopC
Without a population map, all sequences are treated as one population. - Group map (optional but requires population map).
Tab-separated, two columns:
PopA North PopB North PopC South
When provided, EZpopstat runs a two-level hierarchical AMOVA and reports ΦCT, ΦSC and ΦST. Repeated rows with the same population are allowed.
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