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feat: introduce _iqtree_states.csv for compact symbol mapping

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Generates a new CSV output that maps IQ-TREE's compact state symbols to canonical states alongside full-precision empirical frequencies. Updates documentation to clarify that state frequencies sum to 1.0 by design and documents conditional behavior under `--free-loss`. Includes unit tests verifying absent state exclusion, frequency summation, and CSV structure. Also restricts entropy annex resolution to non-monomorphic minorants to eliminate redundant per-genome checks.
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Eric Coissac
2026-08-17 09:38:26 +02:00
parent c6cfdac043
commit 9654201885
6 changed files with 230 additions and 4 deletions
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UserDocMD/usage/phylo.md
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@@ -210,6 +210,7 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
| `<prefix>_sankoff.pg` | `--phyg` | PhyG script | ready-to-run parsimony search |
| `<prefix>_iqtree.model` | `--iqtree` | IQ-TREE model file | custom ML substitution model |
| `<prefix>_iqtree.fasta` | `--iqtree` | FASTA | alignment recoded for that model |
| `<prefix>_iqtree_states.csv` | `--iqtree` | CSV table | maps `_iqtree.model`/`_iqtree.fasta`'s compact state symbols back to `_sankoff_matrix.csv`'s alphabet |
**`_sankoff_matrix.csv`** — header `state,0,A,C,M,G,R,S,V,T,W,Y,H,K,D,B,N`: the 16 symbols are IUPAC codes for the 16 subsets of the 4 possible central bases (bit 0=A, 1=C, 2=G, 3=T), `0` standing for the empty/absent state (not `-`, to avoid colliding with external tools' own gap syntax). One row per source state, one value per destination state, cost $-\ln P(a,b)$, 4 decimals.
@@ -235,3 +236,5 @@ Matrix layout (`_dist.csv`, `_shared.csv`, and every other "CSV matrix" below):
```
iqtree3 -s <prefix>_iqtree.fasta --seqtype MORPH -m <prefix>_iqtree.model+ASC --prefix <prefix>_iqtree -T AUTO
```
**`_iqtree_states.csv`** (`--iqtree`) — one row per state actually kept in `_iqtree.model`/`_iqtree.fasta` (header `iqtree_symbol,canonical_symbol,frequency`): `iqtree_symbol` is the compact `0-9A-F` symbol as written in those two files, `canonical_symbol` is the matching `_sankoff_matrix.csv` state, `frequency` is that state's empirical frequency at full precision (`_iqtree.model`'s own frequency line is rounded to 6 decimals). Under `--free-loss`, absent (`0`/`?`) is never a kept state, so it never appears here. Use this file to identify which real state a given row/column of `_iqtree.model`'s matrix corresponds to — e.g. to check whether a state showing zero exchangeability with everything else is expected (a state combination that never co-occurs with anything else in this data) or worth investigating further.