feat(phylo): add --iqtree-min-freq to filter rare nucleotide states

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.

aloss_nofl_sankoff_params.yaml

@@ -0,0 +1,167 @@
+ratio_ceiling: 0.5
+cardinality_transitions:
+- from: 0
+  to: 0
+  count: 122014779
+  probability: 0.870049812090934
+- from: 0
+  to: 1
+  count: 17966272
+  probability: 0.12811195254940888
+- from: 0
+  to: 2
+  count: 233683
+  probability: 0.001666321505518981
+- from: 0
+  to: 3
+  count: 24109
+  probability: 0.00017191385413811494
+- from: 0
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 1
+  to: 0
+  count: 17966272
+  probability: 0.967023782579572
+- from: 1
+  to: 1
+  count: 602798
+  probability: 0.03244523972983381
+- from: 1
+  to: 2
+  count: 9562
+  probability: 0.0005146688978673966
+- from: 1
+  to: 3
+  count: 303
+  probability: 0.00001630879272681669
+- from: 1
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 2
+  to: 0
+  count: 233683
+  probability: 0.9585500516842502
+- from: 2
+  to: 1
+  count: 9562
+  probability: 0.039222603245442765
+- from: 2
+  to: 2
+  count: 438
+  probability: 0.0017966429848885097
+- from: 2
+  to: 3
+  count: 105
+  probability: 0.00043070208541847837
+- from: 2
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 3
+  to: 0
+  count: 24109
+  probability: 0.9827171564831044
+- from: 3
+  to: 1
+  count: 303
+  probability: 0.012350711286838137
+- from: 3
+  to: 2
+  count: 105
+  probability: 0.004279949455834998
+- from: 3
+  to: 3
+  count: 16
+  probability: 0.0006521827742224758
+- from: 3
+  to: 4
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 0
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 1
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 2
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 3
+  count: 0
+  probability: 0.0
+- from: 4
+  to: 4
+  count: 0
+  probability: 0.0
+composition_transitions:
+- from: 'A'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'C'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'G'
+  count: 0
+  probability: 0.0
+- from: 'A'
+  to: 'T'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'C'
+  to: 'C'
+  count: 96389
+  probability: 0.9663832688335907
+- from: 'C'
+  to: 'G'
+  count: 1290
+  probability: 0.012933368089671353
+- from: 'C'
+  to: 'T'
+  count: 2063
+  probability: 0.020683363076737984
+- from: 'G'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'G'
+  to: 'C'
+  count: 1290
+  probability: 0.005696948820201646
+- from: 'G'
+  to: 'G'
+  count: 222720
+  probability: 0.9835848381669073
+- from: 'G'
+  to: 'T'
+  count: 2427
+  probability: 0.010718213012891003
+- from: 'T'
+  to: 'A'
+  count: 0
+  probability: 0.0
+- from: 'T'
+  to: 'C'
+  count: 2063
+  probability: 0.007305266661709142
+- from: 'T'
+  to: 'G'
+  count: 2427
+  probability: 0.008594223067362136
+- from: 'T'
+  to: 'T'
+  count: 277909
+  probability: 0.9841005102709287