Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
Replaces premature exponentiation-based row normalization with log-sum-exp arithmetic to prevent tiny probabilities from collapsing to exactly zero. This eliminates spurious infinite costs for valid but rare transitions while preserving correct IEEE 754 semantics for genuinely unobserved pairs. Adds explicit guards against NaN in degenerate rows and includes a regression test verifying finite costs for probabilities as low as 1e-200.
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.
Eric Coissac