Implement SNP distance models with gamma correction and PHYLIP output

Renames the CLI flag from --metric to --distance and introduces eight closed-form SNP distance models with optional Jin-Nei gamma correction. Integrates the ndarray crate for matrix operations and adds relaxed PHYLIP output formatting. Updates architecture and theory documentation to cover the new sparse matrix variants, algorithmic fixes, and distance metric implementations.
2026-08-28 21:54:19 +02:00
parent 0b40d2d0da
commit 4f34a646c5
17 changed files with 2199 additions and 73 deletions
@@ -1670,6 +1670,7 @@ version = "1.2.2"
 dependencies = [
 "clap",
 "csv",
+ "ndarray",
 "obifastwrite",
 "obikalgorithm",
 "obikdump",