EZdist Instructions
EZdist computes pairwise genetic distances from an aligned FASTA file. Gap treatment can be configured as pairwise deletion (recommended) or complete deletion. It produces:
- A tabular pairwise distance matrix computed using either K2P (Kimura 2-Parameter) or p-distance.
- A heatmap PDF coloured by distance values, with sequences ordered by hierarchical clustering.
- A collapsed haplotype FASTA and haplotype assignment table — always produced regardless of the plot mode selected.
For haplotype statistics (H, S, π, Tajima's D, FST, AMOVA) use EZpopstat.
- Aligned FASTA file: All sequences must be the same length
(i.e. pre-aligned). One sequence per species or haplotype.
Accepted extensions:
.fasta, .fa, .fsa, .fas, .fna. - FASTA headers are used as taxon labels — keep them short and informative for a clean heatmap.
- Ambiguous bases and gaps (
-,N, etc.) are excluded from pairwise comparisons automatically.
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