src/Cargo.lock

@@ -1689,6 +1689,8 @@ dependencies = [
  "obiread",
  "obiskbuilder",
  "obisys",
+ "serde",
+ "serde_yaml",
  "tracing",
  "tracing-subscriber",
 ]

src/obikmer2/Cargo.toml

@@ -29,6 +29,8 @@ obifastwrite  = { path = "../obifastwrite" }
 obiskbuilder  = { path = "../obiskbuilder" }
 clap          = { version = "4", features = ["derive"] }
 csv           = "1"
+serde         = { version = "1", features = ["derive"] }
+serde_yaml    = "0.9"
 tracing       = "0.1.44"
 tracing-subscriber = { version = "0.3", features = ["fmt", "env-filter"] }
 

src/obikmer2/src/cmd/phylo/args.rs

@@ -38,12 +38,13 @@ impl From<MetricArg> for DistanceMetric {
 /// Partial transfer of `obikmer`'s `phylo` command: the plain distance-metric
 /// path (`--metric`/NJ/UPGMA), annex construction (`--sibling-annex`),
 /// annex diagnostics (`--sibling-stats`, `--sibling-hist`), entropy
-/// reporting (`--shannon`) and SNP pseudo-alignment sampling
+/// reporting (`--shannon`), SNP pseudo-alignment sampling
 /// (`--pseudo-alignment`, `--subsample`, `--free-loss`, `--no-ambiguity`,
-/// `--entropy`/`--entropy-sd`) — everything else sibling-annex-based
-/// (`--sankoff`, `--tnt`/`--phyg`/`--iqtree`, raw SNP distance, family
-/// overlap, ...) stays in `obikmer` until the rest of
-/// `obikphylo::siblings` is reconnected (see the project memory on this).
+/// `--entropy`/`--entropy-sd`) and Sankoff cost-matrix calibration
+/// (`--sankoff`, `--sankoff-ratio-ceiling`) — everything else sibling-annex-based
+/// (`--tnt`/`--phyg`/`--iqtree`, raw SNP distance, family overlap, ...)
+/// stays in `obikmer` until the rest of `obikphylo::siblings` is
+/// reconnected (see the project memory on this).
 #[derive(Args)]
 pub struct PhyloArgs {
     /// Index directory
@@ -124,6 +125,23 @@ pub struct PhyloArgs {
     #[arg(long)]
     pub entropy_sd: Option<f64>,
 
+    /// Calibrate a 16-state Sankoff cost matrix (and its matching
+    /// pseudo-alignment) from an already-built sibling annex — requires
+    /// `--subsample <N>`, and shares `--free-loss`/`--no-ambiguity`/
+    /// `--entropy`/`--entropy-sd` with `--pseudo-alignment` (one draw, same
+    /// selection feeds both the alignment and every calibration tally).
+    #[arg(long)]
+    pub sankoff: bool,
+
+    /// Exclude genome pairs whose raw SNP ratio exceeds this value from the
+    /// base-pair (composition) calibration `--sankoff` pools — a pair this
+    /// close to substitution saturation carries no information about the
+    /// true substitution spectrum. Does *not* gate the cardinality
+    /// calibration (see `obikphylo::siblings::CardinalityTally`'s own
+    /// docs for why).
+    #[arg(long, default_value = "0.5")]
+    pub sankoff_ratio_ceiling: f64,
+
     /// Distance metric to compute
     #[arg(long, value_enum, default_value = "jaccard")]
     pub metric: MetricArg,

src/obikmer2/src/cmd/phylo/mod.rs

@@ -1,15 +1,21 @@
 mod args;
+mod sankoff;
 
 use std::io::{self, BufWriter, Write};
 use std::sync::Arc;
 
 use obikidxcache::index_cache::IndexCache;
 use obikindex::KmerIndex;
-use obikphylo::siblings::{EntropyBias, SiblingExt};
+use obikphylo::siblings::{
+    EntropyBias, SiblingExt, cardinality_transition_probs, composition_transition_probs,
+    pairwise_cost_matrix,
+};
 use obikphylo::{Metrics, neighbor_joining, upgma};
 use obisys::{Reporter, Stage};
 use tracing::info;
 
+use sankoff::{write_sankoff_alignment_fasta, write_sankoff_matrix_csv, write_sankoff_params};
+
 pub use args::PhyloArgs;
 
 pub fn run(args: PhyloArgs) {
@@ -152,14 +158,8 @@ pub fn run(args: PhyloArgs) {
         info!("entropy report → {path}");
     }
 
-    // ── SNP pseudo-alignment (`--pseudo-alignment`) ─────────────────────────────
-    if args.pseudo_alignment {
-        let Some(subsample_n) = args.subsample else {
-            eprintln!("error: --pseudo-alignment requires --subsample <N>");
-            std::process::exit(1);
-        };
-        // Same activation rule as `--shannon`'s own entropy-biased path
-        // would use: either flag given activates biasing, the other
+    // Shared by `--pseudo-alignment` and `--sankoff` — same activation rule:
+    // either flag given activates entropy-biased sampling, the other
     // defaults to 1.0/0.5.
     let entropy_bias = if args.entropy.is_some() || args.entropy_sd.is_some() {
         Some(EntropyBias {
@@ -170,6 +170,13 @@ pub fn run(args: PhyloArgs) {
         None
     };
 
+    // ── SNP pseudo-alignment (`--pseudo-alignment`) ─────────────────────────────
+    if args.pseudo_alignment {
+        let Some(subsample_n) = args.subsample else {
+            eprintln!("error: --pseudo-alignment requires --subsample <N>");
+            std::process::exit(1);
+        };
+
         info!("sampling SNP pseudo-alignment (target {subsample_n} site(s))");
         let t = Stage::start("pseudo_alignment");
         let alignment = cache
@@ -194,6 +201,46 @@ pub fn run(args: PhyloArgs) {
         info!("pseudo-alignment ({n_sites} site(s), {} genome(s)) → {path}", alignment.genome_indices.len());
     }
 
+    // ── Sankoff cost-matrix calibration (`--sankoff`) ───────────────────────────
+    if args.sankoff {
+        let Some(subsample_n) = args.subsample else {
+            eprintln!("error: --sankoff requires --subsample <N>");
+            std::process::exit(1);
+        };
+
+        info!("sampling Sankoff calibration bundle (target {subsample_n} site(s))");
+        let t = Stage::start("sankoff_bundle");
+        let bundle = cache
+            .sankoff_bundle(
+                subsample_n,
+                args.free_loss,
+                args.no_ambiguity,
+                &exclude_mask,
+                entropy_bias,
+                args.sankoff_ratio_ceiling,
+            )
+            .unwrap_or_else(|e| {
+                eprintln!("error computing Sankoff calibration bundle: {e}");
+                std::process::exit(1);
+            });
+        rep.push(t.stop());
+
+        let p_card = cardinality_transition_probs(&bundle.cardinality_tally);
+        let p_comp = composition_transition_probs(&bundle.base_pair_tally);
+        let matrix = pairwise_cost_matrix(&p_card, &p_comp, args.free_loss);
+
+        write_sankoff_matrix_csv(&matrix, &args.output);
+        write_sankoff_params(
+            &bundle.cardinality_tally,
+            &p_card,
+            &bundle.base_pair_tally,
+            &p_comp,
+            args.sankoff_ratio_ceiling,
+            &args.output,
+        );
+        write_sankoff_alignment_fasta(&bundle.alignment, &labels, &args.output, args.free_loss);
+    }
+
     info!("computing {:?} distances for {} genome(s)", args.metric, n);
 
     let need_shared = args.shared_kmers || args.nj || args.upgma;

src/obikmer2/src/cmd/phylo/sankoff.rs

@@ -0,0 +1,168 @@
+//! Output writers for `--sankoff` — no calibration logic here, just
+//! formatting: `obikphylo::siblings::SiblingExt::sankoff_bundle` and the
+//! `cardinality_transition_probs`/`composition_transition_probs`/
+//! `pairwise_cost_matrix` calibration functions do all the actual work in
+//! `mod.rs`, this module only serialises their results.
+
+use std::io::{BufWriter, Write};
+use std::path::PathBuf;
+
+use obifastwrite::{JsonVal, write_record};
+use obikphylo::siblings::{BasePairTally, CardinalityTally, SnpAlignment};
+use tracing::info;
+
+// ── Sankoff pseudo-alignment → FASTA ────────────────────────────────────────
+//
+// Same data as `--pseudo-alignment`'s output (`SnpAlignment`/
+// `snp_pseudo_alignment`), re-coded so its symbols match the accompanying
+// `--sankoff` matrix output exactly: `0` for the empty/absent state instead
+// of `-`, which TNT/PhyG would otherwise read as their own gap character
+// rather than our "family absent" state. Unless `free_loss` (`--free-loss`)
+// is set, in which case `∅` is recoded to `?` instead — TNT/PhyG's own
+// missing-data symbol, deliberately *not* `-` (still gap/indel semantics in
+// both tools) — so non-detection costs nothing rather than being scored as
+// an ordinary, calibrated state transition.
+
+pub(super) fn write_sankoff_alignment_fasta(
+    alignment: &SnpAlignment,
+    labels: &[String],
+    output: &Option<PathBuf>,
+    free_loss: bool,
+) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff.fasta", p.display()))
+        .unwrap_or_else(|| "sankoff.fasta".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    let absent_symbol = if free_loss { b'?' } else { b'0' };
+    let n_sites = alignment.sequences.first().map_or(0, Vec::len);
+    for (&g, seq) in alignment.genome_indices.iter().zip(alignment.sequences.iter()) {
+        let recoded: Vec<u8> = seq.iter().map(|&b| if b == b'-' { absent_symbol } else { b }).collect();
+        write_record(&recoded, &labels[g], &[("n_sites", JsonVal::Num(n_sites as u64))], &mut f)
+            .unwrap_or_else(|e| {
+                eprintln!("error writing {path}: {e}");
+                std::process::exit(1);
+            });
+    }
+    info!("Sankoff pseudo-alignment ({n_sites} site(s)) → {path}");
+}
+
+// ── Sankoff cost matrix → CSV ────────────────────────────────────────────────
+//
+// 16 states indexed by bitmask (bit 0=A, 1=C, 2=G, 3=T; state 0 is `∅`),
+// matching the convention used for `--pseudo-alignment`'s IUPAC-coded output
+// and for the external TNT/PhyG scripts this feeds.
+
+/// IUPAC ambiguity code per state (same mapping
+/// `obikphylo::siblings::algorithms::masking::iupac_code` uses internally
+/// for `--pseudo-alignment`), with `0` standing in for the empty state (`-`
+/// would collide with TNT/PhyG's own gap/range syntax). Bit order: 0=A,
+/// 1=C, 2=G, 3=T. This project's canonical alphabet for every Sankoff
+/// export (`--tnt`/`--phyg`/`--iqtree` each recode it to their own alphabet
+/// at their own adapter boundary, rather than using it directly).
+pub(super) const STATE_SYMBOL: [char; 16] = [
+    '0', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N',
+];
+
+pub(super) fn write_sankoff_matrix_csv(matrix: &[[f64; 16]; 16], output: &Option<PathBuf>) {
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_matrix.csv", p.display()))
+        .unwrap_or_else(|| "sankoff_matrix.csv".into());
+    let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    }));
+    write!(f, "state").unwrap();
+    for sym in STATE_SYMBOL { write!(f, ",{sym}").unwrap(); }
+    writeln!(f).unwrap();
+    for (s, row) in matrix.iter().enumerate() {
+        write!(f, "{}", STATE_SYMBOL[s]).unwrap();
+        for cost in row { write!(f, ",{cost:.4}").unwrap(); }
+        writeln!(f).unwrap();
+    }
+    info!("Sankoff cost matrix → {path}");
+}
+
+// ── Sankoff calibration parameters → YAML report ────────────────────────────
+//
+// Everything `--sankoff` estimates from real data, in one durable,
+// machine-readable file: the cardinality and base-pair transition tallies
+// (raw counts, not just the derived probabilities) — costs are a modelling
+// choice built *from* the counts, and reproducing/re-deriving them later
+// needs the counts, not just their current derived value.
+
+#[derive(serde::Serialize)]
+struct CardinalityTransition {
+    from: usize,
+    to: usize,
+    count: u64,
+    probability: f64,
+}
+
+#[derive(serde::Serialize)]
+struct CompositionTransition {
+    from: char,
+    to: char,
+    count: u64,
+    probability: f64,
+}
+
+#[derive(serde::Serialize)]
+struct SankoffParamsReport {
+    ratio_ceiling: f64,
+    cardinality_transitions: Vec<CardinalityTransition>,
+    composition_transitions: Vec<CompositionTransition>,
+}
+
+pub(super) fn write_sankoff_params(
+    card_tally: &CardinalityTally,
+    p_card: &[[f64; 5]; 5],
+    base_tally: &BasePairTally,
+    p_comp: &[[f64; 4]; 4],
+    ratio_ceiling: f64,
+    output: &Option<PathBuf>,
+) {
+    const BASE_LETTER: [char; 4] = ['A', 'C', 'G', 'T'];
+
+    let mut cardinality_transitions = Vec::with_capacity(25);
+    for a in 0..5 {
+        for b in 0..5 {
+            cardinality_transitions.push(CardinalityTransition {
+                from: a,
+                to: b,
+                count: card_tally.counts[a][b],
+                probability: p_card[a][b],
+            });
+        }
+    }
+
+    let mut composition_transitions = Vec::with_capacity(16);
+    for a in 0..4 {
+        for b in 0..4 {
+            let count = if a == b { base_tally.same[a] } else { base_tally.counts[a][b] };
+            composition_transitions.push(CompositionTransition {
+                from: BASE_LETTER[a],
+                to: BASE_LETTER[b],
+                count,
+                probability: p_comp[a][b],
+            });
+        }
+    }
+
+    let report = SankoffParamsReport { ratio_ceiling, cardinality_transitions, composition_transitions };
+
+    let path = output.as_ref()
+        .map(|p| format!("{}_sankoff_params.yaml", p.display()))
+        .unwrap_or_else(|| "sankoff_params.yaml".into());
+    let f = std::fs::File::create(&path).unwrap_or_else(|e| {
+        eprintln!("error creating {path}: {e}");
+        std::process::exit(1);
+    });
+    serde_yaml::to_writer(f, &report).unwrap_or_else(|e| {
+        eprintln!("error writing {path}: {e}");
+        std::process::exit(1);
+    });
+    info!("Sankoff calibration parameters → {path}");
+}

src/obikphylo/src/siblings/algorithms/cardcomp.rs

@@ -22,7 +22,7 @@ use super::pairwise::{BasePairTally, CardinalityTally};
 /// Row-stochastic 5×5 cardinality transition probabilities (`0..=4`),
 /// diagonal included ("stay at the same cardinality"), from
 /// [`CardinalityTally`]'s pooled co-occurrence counts.
-pub(crate) fn cardinality_transition_probs(tally: &CardinalityTally) -> [[f64; 5]; 5] {
+pub fn cardinality_transition_probs(tally: &CardinalityTally) -> [[f64; 5]; 5] {
     let mut p = [[0.0f64; 5]; 5];
     for a in 0..5 {
         let row_sum: u64 = tally.counts[a].iter().sum();
@@ -40,7 +40,7 @@ pub(crate) fn cardinality_transition_probs(tally: &CardinalityTally) -> [[f64; 5
 /// (`A,C,G,T`), diagonal included ("stay the same base"), from
 /// [`BasePairTally`]'s pooled substitution (off-diagonal) and agreement
 /// (`same`, diagonal) counts — unambiguous, cardinality-1 loci only.
-pub(crate) fn composition_transition_probs(tally: &BasePairTally) -> [[f64; 4]; 4] {
+pub fn composition_transition_probs(tally: &BasePairTally) -> [[f64; 4]; 4] {
     let mut p = [[0.0f64; 4]; 4];
     for a in 0..4 {
         let row_sum = tally.same[a] + (0..4).map(|b| tally.counts[a][b]).sum::<u64>();
@@ -143,7 +143,7 @@ fn best_pairing_cost(lost: &[u8], gained: &[u8], p_comp: &[[f64; 4]; 4]) -> f64
 /// factor dropped, cost is driven only by composition matching
 /// (shared-base retention and paired substitutions), never by a state
 /// pair's cardinality difference alone.
-pub(crate) fn pairwise_cost_matrix(
+pub fn pairwise_cost_matrix(
     p_card: &[[f64; 5]; 5],
     p_comp: &[[f64; 4]; 4],
     free_loss: bool,

src/obikphylo/src/siblings/algorithms/mod.rs

@@ -27,17 +27,18 @@ mod subsample;
 
 use obikidxcache::index_cache::IndexCache;
 
+pub use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix};
 pub use alignment::SnpAlignment;
+pub use pairwise::{BasePairTally, CardinalityTally, RawSnpDistanceOutput};
+pub use sankoff::SankoffBundle;
 pub use stats::SiblingAnnexStats;
 pub use subsample::EntropyBias;
 
 pub(crate) use alignment::snp_pseudo_alignment;
 pub(crate) use annex::build_layer_sibling_annex;
-pub(crate) use cardcomp::{cardinality_transition_probs, composition_transition_probs, pairwise_cost_matrix};
 pub(crate) use entropy::{ensure_layer_entropy_annex, family_entropy, family_entropy_4, iter_full_entropy};
 pub(crate) use family_scan::{Selection, scan_layer_families};
-pub(crate) use pairwise::{BasePairTally, CardinalityTally, RawSnpDistanceOutput};
-pub(crate) use sankoff::{SankoffBundle, sankoff_bundle};
+pub(crate) use sankoff::sankoff_bundle;
 pub(crate) use stats::{sibling_annex_stats, sibling_family_size_histogram};
 pub(crate) use subsample::sample_index;
 

src/obikphylo/src/siblings/algorithms/pairwise.rs

@@ -178,8 +178,9 @@ impl PairwiseTally {
 }
 
 /// Raw p-distance restricted to loci that are single-copy in **both**
-/// genomes of a pair — see `PairwiseTally`'s module docs.
-pub(crate) struct RawSnpDistanceOutput {
+/// genomes of a pair — see `PairwiseTally`'s module docs. `pub`: part of
+/// [`super::SankoffBundle`]'s public signature.
+pub struct RawSnpDistanceOutput {
     /// n×n count of eligible loci where the two genomes' single forms differ.
     pub snp: Array2<u64>,
     /// n×n count of eligible loci where the two genomes' single forms agree.
@@ -187,8 +188,9 @@ pub(crate) struct RawSnpDistanceOutput {
 }
 
 /// Symmetric 6-category base-pair substitution tally (indexed
-/// `0=A,1=C,2=G,3=T`), pooled over [`PairwiseTally::included`] genome pairs.
-pub(crate) struct BasePairTally {
+/// `0=A,1=C,2=G,3=T`), pooled over [`PairwiseTally::included`] genome
+/// pairs. `pub`: part of [`super::SankoffBundle`]'s public signature.
+pub struct BasePairTally {
     /// `counts[a][b] == counts[b][a]` = number of eligible loci, pooled over
     /// included genome pairs, where the two genomes' single forms are `a`
     /// and `b`. Diagonal always `0` — an `a == b` locus is counted in
@@ -207,8 +209,9 @@ pub(crate) struct BasePairTally {
 /// [`PairwiseTally::cardinality_tally`]'s own docs for why this is *not*
 /// gated by `ratio_ceiling` the way [`BasePairTally`] is), restricted to
 /// variable families (`family_size() >= 2`) — matching
-/// `snp_pseudo_alignment`'s own scope.
-pub(crate) struct CardinalityTally {
+/// `snp_pseudo_alignment`'s own scope. `pub`: part of
+/// [`super::SankoffBundle`]'s public signature.
+pub struct CardinalityTally {
     /// `counts[a][b] == counts[b][a]` = number of family sites, pooled over
     /// included genome pairs, where one genome's family cardinality is `a`
     /// and the other's is `b`. Diagonal is real data here (both genomes at

src/obikphylo/src/siblings/algorithms/sankoff.rs

@@ -19,8 +19,9 @@ use super::subsample::{EntropyBias, sample_index};
 
 /// Every output the `--sankoff`/`--tnt`/`--phyg`/`--iqtree` pipeline needs,
 /// computed together from one shared, possibly-subsampled/entropy-biased
-/// selection — see the module docs.
-pub(crate) struct SankoffBundle {
+/// selection — see the module docs. `pub`: part of the public signature of
+/// [`crate::siblings::extensions::SiblingExt::sankoff_bundle`].
+pub struct SankoffBundle {
     pub alignment: SnpAlignment,
     pub raw: RawSnpDistanceOutput,
     pub base_pair_tally: BasePairTally,

src/obikphylo/src/siblings/extensions/sibling_ext.rs

@@ -14,9 +14,10 @@ use obikindex::{OKIError, OKIResult};
 use obisys::progress_bar;
 
 use crate::siblings::algorithms::{
-    EntropyBias, Selection, SiblingAnnexStats, SnpAlignment, build_layer_sibling_annex,
-    family_entropy, family_entropy_4, is_fast_mode, scan_layer_families,
-    sibling_annex_stats, sibling_family_size_histogram, snp_pseudo_alignment,
+    EntropyBias, SankoffBundle, Selection, SiblingAnnexStats, SnpAlignment,
+    build_layer_sibling_annex, family_entropy, family_entropy_4, is_fast_mode,
+    sankoff_bundle, scan_layer_families, sibling_annex_stats, sibling_family_size_histogram,
+    snp_pseudo_alignment,
 };
 use crate::siblings::extensions::SiblingBuilder;
 use crate::siblings::ENTROPY_ANNEX_FILE_NAME;
@@ -94,6 +95,32 @@ pub trait SiblingExt {
     /// use [`sibling_family_size_histogram`](Self::sibling_family_size_histogram)
     /// instead when only the global histogram is needed.
     fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats>;
+
+    /// Fused entry point for the `--sankoff`/`--tnt`/`--phyg`/`--iqtree`
+    /// pipeline: one shared, possibly-subsampled/entropy-biased selection
+    /// (`n`/`free_loss`/`no_ambiguity`/`excluded`/`entropy_bias` — same
+    /// meaning as [`snp_pseudo_alignment`](Self::snp_pseudo_alignment)'s
+    /// own) drives a single scan producing the pseudo-alignment *and* every
+    /// tally the Sankoff cost-matrix calibration
+    /// (`crate::siblings::cardinality_transition_probs`/
+    /// `composition_transition_probs`/`pairwise_cost_matrix`) needs —
+    /// never two independent draws of the same index. `ratio_ceiling`
+    /// (`--sankoff-ratio-ceiling`) excludes genome pairs too close to
+    /// substitution saturation from `SankoffBundle::base_pair_tally`'s
+    /// pool (a saturated pair's base composition is noise, not signal) —
+    /// `SankoffBundle::cardinality_tally` is *not* gated by it (see
+    /// `crate::siblings::CardinalityTally`'s own docs for why that
+    /// wouldn't make sense: cardinality reflects each genome's own
+    /// coverage/duplication structure, not the pair's mutual divergence).
+    fn sankoff_bundle(
+        &self,
+        n: usize,
+        free_loss: bool,
+        no_ambiguity: bool,
+        excluded: &[bool],
+        entropy_bias: Option<EntropyBias>,
+        ratio_ceiling: f64,
+    ) -> OKIResult<SankoffBundle>;
 }
 
 impl SiblingExt for IndexCache {
@@ -226,4 +253,16 @@ impl SiblingExt for IndexCache {
     fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {
         sibling_annex_stats(self)
     }
+
+    fn sankoff_bundle(
+        &self,
+        n: usize,
+        free_loss: bool,
+        no_ambiguity: bool,
+        excluded: &[bool],
+        entropy_bias: Option<EntropyBias>,
+        ratio_ceiling: f64,
+    ) -> OKIResult<SankoffBundle> {
+        sankoff_bundle(self, n, free_loss, no_ambiguity, excluded, entropy_bias, ratio_ceiling)
+    }
 }

src/obikphylo/src/siblings/mod.rs

@@ -29,7 +29,11 @@ mod siblingannex;
 pub(crate) use entropy_annex::{ENTROPY_ANNEX_FILE_NAME, EntropyAnnex, EntropyAnnexBuilder};
 pub(crate) use siblingannex::{FamilyMask, SiblingAnnex, SiblingAnnexBuilder};
 
-pub use algorithms::{EntropyBias, SiblingAnnexStats, SnpAlignment};
+pub use algorithms::{
+    BasePairTally, CardinalityTally, EntropyBias, RawSnpDistanceOutput, SankoffBundle,
+    SiblingAnnexStats, SnpAlignment, cardinality_transition_probs, composition_transition_probs,
+    pairwise_cost_matrix,
+};
 pub use extensions::SiblingExt;
 
 pub(crate) const ANNEX_FILE_NAME: &str = "siblings.psib";