Add phylogenetic CLI options for family overlap and missing data

Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.

sankoff_params.yaml

@@ -2,166 +2,166 @@ ratio_ceiling: 0.5
 cardinality_transitions:
 - from: 0
   to: 0
-  count: 117158166
-  probability: 0.8249649657257814
+  count: 37622567
+  probability: 0.7765461217831444
 - from: 0
   to: 1
-  count: 13707223
-  probability: 0.09651891232567299
+  count: 6977400
+  probability: 0.14401656617768033
 - from: 0
   to: 2
-  count: 10934100
-  probability: 0.07699206755884405
+  count: 3744558
+  probability: 0.0772893033240408
 - from: 0
   to: 3
-  count: 193315
-  probability: 0.0013612205430842902
+  count: 91083
+  probability: 0.0018799926759482985
 - from: 0
   to: 4
-  count: 23125
-  probability: 0.00016283384661730445
+  count: 12985
+  probability: 0.0002680160391861122
 - from: 1
   to: 0
-  count: 13707223
-  probability: 0.8980473700324103
+  count: 6977400
+  probability: 0.820630384894398
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   to: 1
-  count: 1043692
-  probability: 0.06837890181868832
+  count: 1018042
+  probability: 0.1197346000370715
 - from: 1
   to: 2
-  count: 507953
-  probability: 0.033279232106318904
+  count: 502624
+  probability: 0.05911493200578466
 - from: 1
   to: 3
-  count: 4270
-  probability: 0.0002797548613631216
+  count: 4197
+  probability: 0.000493620220340211
 - from: 1
   to: 4
   count: 225
-  probability: 0.000014741181219368235
+  probability: 0.000026462842405658202
 - from: 2
   to: 0
-  count: 10934100
-  probability: 0.9551033885158036
+  count: 3744558
+  probability: 0.8804244781723005
 - from: 2
   to: 1
-  count: 507953
-  probability: 0.04437014765794788
+  count: 502624
+  probability: 0.11817749195415704
 - from: 2
   to: 2
-  count: 5241
-  probability: 0.00045780602511512846
+  count: 5162
+  probability: 0.0012136949558066439
 - from: 2
   to: 3
-  count: 690
-  probability: 0.000060272115498843476
+  count: 688
+  probability: 0.0001617632951559417
 - from: 2
   to: 4
   count: 96
-  probability: 8.385685634621701e-6
+  probability: 0.00002257162257989884
 - from: 3
   to: 0
-  count: 193315
-  probability: 0.9743748708410829
+  count: 91083
+  probability: 0.9478728718311618
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   to: 1
-  count: 4270
-  probability: 0.021522285898618442
+  count: 4197
+  probability: 0.04367689297756317
 - from: 3
   to: 2
-  count: 690
-  probability: 0.0034778401100812
+  count: 688
+  probability: 0.007159805186696083
 - from: 3
   to: 3
   count: 98
-  probability: 0.0004939541025912429
+  probability: 0.0010198559713607792
 - from: 3
   to: 4
   count: 26
-  probability: 0.0001310490476262481
+  probability: 0.00027057403321816594
 - from: 4
   to: 0
-  count: 23125
-  probability: 0.9846291407647109
+  count: 12985
+  probability: 0.972950696838004
 - from: 4
   to: 1
   count: 225
-  probability: 0.009580175423656646
+  probability: 0.01685898396523303
 - from: 4
   to: 2
   count: 96
-  probability: 0.004087541514093502
+  probability: 0.0071931664918327585
 - from: 4
   to: 3
   count: 26
-  probability: 0.0011070424934003236
+  probability: 0.0019481492582047056
 - from: 4
   to: 4
   count: 14
-  probability: 0.0005960998041386358
+  probability: 0.0010490034467256107
 composition_transitions:
 - from: 'A'
   to: 'A'
-  count: 162260
-  probability: 0.47062167539692207
+  count: 157182
+  probability: 0.46648741052031767
 - from: 'A'
   to: 'C'
-  count: 27810
-  probability: 0.08066059899413536
+  count: 27305
+  probability: 0.08103624298111281
 - from: 'A'
   to: 'G'
-  count: 130153
-  probability: 0.3774979842101294
+  count: 128548
+  probability: 0.38150693875612857
 - from: 'A'
   to: 'T'
-  count: 24555
-  probability: 0.07121974139881315
+  count: 23913
+  probability: 0.07096940774244097
 - from: 'C'
   to: 'A'
-  count: 27810
-  probability: 0.07790832534920075
+  count: 27305
+  probability: 0.07823849488677553
 - from: 'C'
   to: 'C'
-  count: 184633
-  probability: 0.5172401234879174
+  count: 179118
+  probability: 0.5132365034656459
 - from: 'C'
   to: 'G'
-  count: 19637
-  probability: 0.05501207424963161
+  count: 19392
+  probability: 0.055564947549692406
 - from: 'C'
   to: 'T'
-  count: 124878
-  probability: 0.3498394769132503
+  count: 123182
+  probability: 0.3529600540978862
 - from: 'G'
   to: 'A'
-  count: 130153
-  probability: 0.36057158212891627
+  count: 128548
+  probability: 0.3637269077214298
 - from: 'G'
   to: 'C'
-  count: 19637
-  probability: 0.054401697680925745
+  count: 19392
+  probability: 0.05486971555009776
 - from: 'G'
   to: 'G'
-  count: 184557
-  probability: 0.5112906308956874
+  count: 179245
+  probability: 0.5071742039901647
 - from: 'G'
   to: 'T'
-  count: 26616
-  probability: 0.07373608929447062
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+  probability: 0.07422917273830779
 - from: 'T'
   to: 'A'
-  count: 24555
-  probability: 0.07337692220342934
+  count: 23913
+  probability: 0.07307212790143376
 - from: 'T'
   to: 'C'
-  count: 124878
-  probability: 0.3731689387464813
+  count: 123182
+  probability: 0.3764132839524281
 - from: 'T'
   to: 'G'
-  count: 26616
-  probability: 0.07953574267426085
+  count: 26234
+  probability: 0.08016452153080807
 - from: 'T'
   to: 'T'
-  count: 158593
-  probability: 0.4739183963758285
+  count: 153923
+  probability: 0.4703500666153301