rename distance subcommand to phylo

Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
2026-08-15 10:07:03 +02:00
parent 79346c0c86
commit dd889854cb
19 changed files with 49 additions and 46 deletions
@@ -289,14 +289,14 @@ obikmer dump myindex --head 100
 obikmer dump myindex --head 20 --ingroup "species=Betula_nana" --min-count 1
 ```

-### `distance --presence-threshold N`
+### `phylo --presence-threshold N`

 When computing Jaccard distance on a **count index**, a k-mer is considered present in a genome if its count is ≥ N (default 1).
 This option is independent of the `--presence-threshold` used in filtering.

 ```sh
 # Jaccard treating kmers with count ≥ 2 as present
-obikmer distance myindex --metric jaccard --presence-threshold 2
+obikmer phylo myindex --metric jaccard --presence-threshold 2
 ```

 This parameter has no effect on presence/absence indexes (where values are already 0/1) or on metrics other than Jaccard.