diff --git a/Cargo.lock b/Cargo.lock
index ac3dc86..88cf20c 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -98,8 +98,8 @@ version = "0.1.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "82f6aeea286b8eb4dd3431a1be1b59d290ace00f5bfd8e2a159bc2a05e2c1667"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 3.0.3",
 ]
 
@@ -141,24 +141,24 @@ checksum = "9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8"
 
 [[package]]
 name = "bio"
-version = "2.3.0"
+version = "4.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "add46f280e82963d4abb6f2c78f491a1f45be23ba27516856a1efbf194107bb7"
+checksum = "7ec70754e9fc444b545c0f4e3ac5547885dd83f297d642be4a260672aa59610b"
 dependencies = [
- "anyhow",
  "approx",
  "bio-types",
- "bit-set",
+ "bit-set 0.10.0",
  "bv",
  "bytecount",
  "csv",
  "custom_derive",
+ "derefable",
  "editdistancek",
  "enum-map",
  "fxhash",
+ "getset",
  "itertools 0.14.0",
  "itertools-num",
- "lazy_static",
  "multimap",
  "ndarray",
  "newtype_derive",
@@ -170,8 +170,8 @@ dependencies = [
  "serde",
  "serde_derive",
  "statrs",
- "strum 0.26.3",
- "strum_macros 0.26.4",
+ "strum",
+ "strum_macros 0.27.2",
  "thiserror 2.0.20",
  "triple_accel",
  "vec_map",
@@ -196,7 +196,16 @@ version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "08807e080ed7f9d5433fa9b275196cfc35414f66a0c79d864dc51a0d825231a3"
 dependencies = [
- "bit-vec",
+ "bit-vec 0.8.0",
+]
+
+[[package]]
+name = "bit-set"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "09ec2f926cc3060f09db9ebc5b52823d85268d24bb917e472c0c4bea35780a7d"
+dependencies = [
+ "bit-vec 0.9.1",
 ]
 
 [[package]]
@@ -205,6 +214,15 @@ version = "0.8.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "5e764a1d40d510daf35e07be9eb06e75770908c27d411ee6c92109c9840eaaf7"
 
+[[package]]
+name = "bit-vec"
+version = "0.9.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b71798fca2c1fe1086445a7258a4bc81e6e49dcd24c8d0dd9a1e57395b603f51"
+dependencies = [
+ "serde",
+]
+
 [[package]]
 name = "bitflags"
 version = "2.13.1"
@@ -742,8 +760,8 @@ checksum = "0d00b9596d185e565c2207a0b01f8bd1a135483d02d9b7b0a54b11da8d53412e"
 dependencies = [
  "fnv",
  "ident_case",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "strsim",
  "syn 2.0.119",
 ]
@@ -755,7 +773,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "fc34b93ccb385b40dc71c6fceac4b2ad23662c7eeb248cf10d529b7e055b6ead"
 dependencies = [
  "darling_core",
- "quote",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -773,14 +791,25 @@ dependencies = [
  "parking_lot_core",
 ]
 
+[[package]]
+name = "derefable"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e519abf1289075763071c981958e89948b079fc54962617a0e6413d9ce44cbe7"
+dependencies = [
+ "proc-macro2 0.4.30",
+ "quote 0.6.13",
+ "syn 0.15.44",
+]
+
 [[package]]
 name = "derive-new"
 version = "0.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d150dea618e920167e5973d70ae6ece4385b7164e0d799fe7c122dd0a5d912ad"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -800,8 +829,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2d5bcf7b024d6835cfb3d473887cd966994907effbe9227e8c8219824d06c4e8"
 dependencies = [
  "darling",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -853,8 +882,8 @@ version = "0.2.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c6232dd377dcc64799954cbd3a9bb882e9cdc1308ccd87b1c098f1fb2eaf82a8"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 3.0.3",
 ]
 
@@ -915,8 +944,8 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "685adfa4d6f3d765a26bc5dbc936577de9abf756c1feeb3089b01dd395034842"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -935,8 +964,8 @@ version = "0.17.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -971,7 +1000,7 @@ version = "0.14.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6e24cb5a94bcae1e5408b0effca5cd7172ea3c5755049c5f3af4cd283a165298"
 dependencies = [
- "bit-set",
+ "bit-set 0.8.0",
  "regex-automata",
  "regex-syntax",
 ]
@@ -1195,6 +1224,17 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "getset"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6cf442baaabe4213ce7d1239afc26c039180b6456da2cededa316ae2c8a77a77"
+dependencies = [
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
+ "syn 2.0.119",
+]
+
 [[package]]
 name = "gimli"
 version = "0.32.3"
@@ -1554,8 +1594,8 @@ version = "1.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1ec89e9337638ecdc08744df490b221a7399bf8d164eb52a665454e60e075ad6"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -1629,8 +1669,8 @@ version = "0.7.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7cab85a7ed0bd5f0e76d93846e0147172bed2e2d3f859bcc33a8d9699cad1a75"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
 ]
 
 [[package]]
@@ -1795,7 +1835,7 @@ dependencies = [
  "regex",
  "serde",
  "serde-wasm-bindgen",
- "strum 0.27.2",
+ "strum",
  "strum_macros 0.27.2",
  "wasm-bindgen",
 ]
@@ -1887,8 +1927,8 @@ version = "0.3.37"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "77060ebe535362c3da75682cd17b0431017b6e7c5661e714fc69a7ad017d1301"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 3.0.3",
 ]
 
@@ -2039,8 +2079,8 @@ version = "0.1.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e4db6d5580af57bf992f59068d4ea26fd518574ff48d7639b255a36f9de6e7e9"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -2337,6 +2377,15 @@ dependencies = [
  "zerocopy",
 ]
 
+[[package]]
+name = "proc-macro2"
+version = "0.4.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cf3d2011ab5c909338f7887f4fc896d35932e29146c12c8d01da6b22a80ba759"
+dependencies = [
+ "unicode-xid 0.1.0",
+]
+
 [[package]]
 name = "proc-macro2"
 version = "1.0.107"
@@ -2352,8 +2401,8 @@ version = "1.11.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4b45fcc2344c680f5025fe57779faef368840d0bd1f42f216291f0dc4ace4744"
 dependencies = [
- "bit-set",
- "bit-vec",
+ "bit-set 0.8.0",
+ "bit-vec 0.8.0",
  "bitflags",
  "num-traits",
  "rand 0.9.5",
@@ -2383,8 +2432,8 @@ version = "47.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9f10925455d5dde962e3604eade797ba5488644c8ee14a44191e2f2b58980574"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -2394,13 +2443,22 @@ version = "1.2.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "a1d01941d82fa2ab50be1e79e6714289dd7cde78eba4c074bc5a4374f650dfe0"
 
+[[package]]
+name = "quote"
+version = "0.6.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ce23b6b870e8f94f81fb0a363d65d86675884b34a09043c81e5562f11c1f8e1"
+dependencies = [
+ "proc-macro2 0.4.30",
+]
+
 [[package]]
 name = "quote"
 version = "1.0.47"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1fbf4db142a473a8d80c26bbf18454ed458bf8d26c8219c331daecfdbd079001"
 dependencies = [
- "proc-macro2",
+ "proc-macro2 1.0.107",
 ]
 
 [[package]]
@@ -2774,8 +2832,8 @@ version = "1.0.229"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e7a5d71263a5a7d47b41f6b3f06ba276f10cc18b0931f1799f710578e2309348"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 3.0.3",
 ]
 
@@ -3922,12 +3980,6 @@ version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
-[[package]]
-name = "strum"
-version = "0.26.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8fec0f0aef304996cf250b31b5a10dee7980c85da9d759361292b8bca5a18f06"
-
 [[package]]
 name = "strum"
 version = "0.27.2"
@@ -3941,8 +3993,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4c6bee85a5a24955dc440386795aa378cd9cf82acd5f764469152d2270e581be"
 dependencies = [
  "heck",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "rustversion",
  "syn 2.0.119",
 ]
@@ -3954,19 +4006,30 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7695ce3845ea4b33927c055a39dc438a45b059f7c1b3d91d38d10355fb8cbca7"
 dependencies = [
  "heck",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
+[[package]]
+name = "syn"
+version = "0.15.44"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ca4b3b69a77cbe1ffc9e198781b7acb0c7365a883670e8f1c1bc66fba79a5c5"
+dependencies = [
+ "proc-macro2 0.4.30",
+ "quote 0.6.13",
+ "unicode-xid 0.1.0",
+]
+
 [[package]]
 name = "syn"
 version = "2.0.119"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "872831b642d1a07999a962a351ed35b955ea2cfc8f3862091e2a240a84f17297"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "unicode-ident",
 ]
 
@@ -3976,8 +4039,8 @@ version = "3.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "53e9bae58849f64dfa4f5d5ae372c8341f7305f82a3868709269343628b659a3"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "unicode-ident",
 ]
 
@@ -3987,8 +4050,8 @@ version = "0.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "728a70f3dbaf5bab7f0c4b1ac8d7ae5ea60a4b5549c8a5914361c99147a709d2"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -4044,8 +4107,8 @@ version = "1.0.69"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4fee6c4efc90059e10f81e6d42c60a18f76588c3d74cb83a0b242a2b6c7504c1"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -4055,8 +4118,8 @@ version = "2.0.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bc04cd3e1236dd4a98afca4569f2deb3f120e5422a4023be2cb683f8486292af"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 3.0.3",
 ]
 
@@ -4214,8 +4277,8 @@ version = "0.1.31"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7490cfa5ec963746568740651ac6781f701c9c5ea257c58e057f3ba8cf69e8da"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -4300,6 +4363,12 @@ version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b4ac048d71ede7ee76d585517add45da530660ef4390e49b098733c6e897f254"
 
+[[package]]
+name = "unicode-xid"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc"
+
 [[package]]
 name = "unicode-xid"
 version = "0.2.6"
@@ -4404,7 +4473,7 @@ version = "0.2.127"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "77775f8f3f7217702089053b94958f8f54061a3f663417df76e19cbdcca29bc1"
 dependencies = [
- "quote",
+ "quote 1.0.47",
  "wasm-bindgen-macro-support",
 ]
 
@@ -4415,8 +4484,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e11d33f857dc2fb11b8bc75aee111aa9cbeb12cd9f25efd3d4c2a3dd4e235284"
 dependencies = [
  "bumpalo",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
  "wasm-bindgen-shared",
 ]
@@ -4555,8 +4624,8 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2bf7b91fed3fc34781d57f9c6654ea2513bf0a99f7b0b0523c00de1e6efebe1c"
 dependencies = [
  "anyhow",
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
  "wasmtime-internal-component-util",
  "wasmtime-internal-wit-bindgen",
@@ -4663,8 +4732,8 @@ version = "47.0.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "153592e0bed824fc13c6696203fa1bd7bd20eb355316475e39a55f081ef80eca"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -4874,7 +4943,7 @@ dependencies = [
  "serde",
  "serde_derive",
  "serde_json",
- "unicode-xid",
+ "unicode-xid 0.2.6",
  "wasmparser 0.230.0",
 ]
 
@@ -4944,8 +5013,8 @@ version = "0.7.5"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2380878cad4ac9aac1e2435f3eb4020e8374b5f13c296cb75b4620ff8e229154"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
  "synstructure",
 ]
@@ -4956,8 +5025,8 @@ version = "0.8.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "de844c262c8848816172cef550288e7dc6c7b7814b4ee56b3e1553f275f1858e"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
  "synstructure",
 ]
@@ -4977,8 +5046,8 @@ version = "0.8.56"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f2ab42fc20575779bd240faa45f94a74256f755c0fa9e89f0ede20d91d0cdfc1"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -4997,8 +5066,8 @@ version = "0.1.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "11532158c46691caf0f2593ea8358fed6bbf68a0315e80aae9bd41fbade684a1"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
  "synstructure",
 ]
@@ -5042,8 +5111,8 @@ version = "0.10.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6eafa6dfb17584ea3e2bd6e76e0cc15ad7af12b09abdd1ca55961bed9b1063c6"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
@@ -5053,8 +5122,8 @@ version = "0.11.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "625dc425cab0dca6dc3c3319506e6593dcb08a9f387ea3b284dbd52a92c40555"
 dependencies = [
- "proc-macro2",
- "quote",
+ "proc-macro2 1.0.107",
+ "quote 1.0.47",
  "syn 2.0.119",
 ]
 
diff --git a/crates/stringcheese-align/Cargo.toml b/crates/stringcheese-align/Cargo.toml
index 9be9401..f213e79 100644
--- a/crates/stringcheese-align/Cargo.toml
+++ b/crates/stringcheese-align/Cargo.toml
@@ -48,7 +48,7 @@ stringcheese-core = { workspace = true }
 # a plain `cargo build` / `cargo test` / `cargo bench` never pulls it
 # in. Lives in `[dependencies]` (not `[dev-dependencies]`) because Cargo
 # does not allow optional dev-deps.
-bio = { version = "2", default-features = false, optional = true }
+bio = { version = "4", default-features = false, optional = true }
 
 [dev-dependencies]
 stringcheese-corpus = { workspace = true, features = ["alloc"] }