From 19f4ec256722b9572f13874ceb92538b2a7d01b7 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Sat, 12 Sep 2026 17:56:30 +0200 Subject: [PATCH] Add documentation for whole-index distance metrics. Adds documentation describing metrics that operate directly on kmer sets or counts stored in an index, clarifying that they do not require per-locus SNP calling. --- theory-phylogeny-kmer_based-distance_metrics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/theory-phylogeny-kmer_based-distance_metrics.md b/theory-phylogeny-kmer_based-distance_metrics.md index 0bf3735..26459fd 100644 --- a/theory-phylogeny-kmer_based-distance_metrics.md +++ b/theory-phylogeny-kmer_based-distance_metrics.md @@ -1,6 +1,6 @@ # Whole-index distance metrics -These metrics operate on the kmer sets or counts stored in an index directly — no per-locus SNP calling, no sibling annex required. `A`/`B` denote the two genomes being compared; $c_i^A$/$c_i^B$ are their raw counts at kmer $i$, $p_i^A$/$p_i^B$ the corresponding relative frequencies ($p_i = c_i / \sum_j c_j$). +These metrics operate on the kmer sets or counts stored in an index directly — no per-locus SNP calling, no sibling annex required. `A`/`B` denote the two genomes being compared; $c_i^A$ / $c_i^B$ are their raw counts at kmer $i$, $p_i^A$ / $p_i^B$ the corresponding relative frequencies ($p_i = c_i / \sum_j c_j$). | Metric | Definition | | --- | --- |