feat: add phylogenetic analysis CLI command and lazy distance traits

Introduce the `obikphylo` crate to support genome-vs-genome distance matrix computation and phylogenetic tree inference via Neighbor-Joining and UPGMA algorithms. Extend the `obikmer2` CLI with a new `phylo` command that exposes configurable metrics, presence thresholds, and CSV/Newick output options. Refactor `obikindex` to expose trait-based partial aggregation for efficient distance metric finalization without full matrix materialization. Update dependency graphs and remove obsolete storage modules.
2026-08-28 20:11:13 +02:00
parent 4b6005962e
commit 635fc830d1
17 changed files with 696 additions and 97 deletions
@@ -12,10 +12,13 @@ obicompactvec    = { path = "../obicompactvec" }
 obikidxcache     = { path = "../obikidxcache" }
 obiskbuilder     = { path = "../obiskbuilder" }
 obipipeline      = { path = "../obipipeline" }
+kodama           = "0.3.0"
 memmap2          = "0.9"
 ndarray          = "0.17"
+petgraph         = "0.6.4"
 rand             = "0.10"
 rayon            = "1"
+speedytree       = "0.1"
 tracing          = "0.1.44"

 [dev-dependencies]