Replace Sankoff cost matrix with cardinality-composition decomposition
Replaced the legacy Sankoff parsimony pipeline with a new cardinality-composition decomposition that constructs row-normalized transition probability matrices symmetrized via geometric mean. This ensures reversibility, reduces free parameters from 240 to 120, and guarantees a zero diagonal. Tallies are now explicitly restricted to variable families to align with +ASC-corrected alignment populations. Additionally, fixed `--exclude-genome` handling to re-scan surviving sequences and drop newly monomorphic columns, preventing silent data corruption in downstream tree inference tools.
This commit is contained in:
Eric Coissac
+160
-20
@@ -1,27 +1,167 @@
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ratio_ceiling: 0.5
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flank_length_m: 15
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p_hat: 0.010713940022064144
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p_hat_variance: 3.2110559785689563e-10
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n_pairs_included: 158
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n_loci_total: 33008305
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mean_sub_cost: 1.4764371767846869
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c_ctx: 1.7343663443925388
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substitutions:
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- pair: A/C
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cardinality_transitions:
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- from: 0
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to: 0
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count: 117158166
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probability: 0.8249649657257814
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- from: 0
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to: 1
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count: 13707223
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probability: 0.09651891232567299
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- from: 0
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to: 2
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count: 10934100
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probability: 0.07699206755884405
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- from: 0
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to: 3
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count: 193315
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probability: 0.0013612205430842902
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- from: 0
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to: 4
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count: 23125
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probability: 0.00016283384661730445
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- from: 1
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to: 0
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count: 13707223
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probability: 0.8980473700324103
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- from: 1
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to: 1
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count: 1043692
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probability: 0.06837890181868832
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- from: 1
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to: 2
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count: 507953
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probability: 0.033279232106318904
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- from: 1
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to: 3
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count: 4270
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probability: 0.0002797548613631216
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- from: 1
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to: 4
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count: 225
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probability: 0.000014741181219368235
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- from: 2
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to: 0
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count: 10934100
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probability: 0.9551033885158036
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- from: 2
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to: 1
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count: 507953
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probability: 0.04437014765794788
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- from: 2
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to: 2
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count: 5241
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probability: 0.00045780602511512846
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- from: 2
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to: 3
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count: 690
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probability: 0.000060272115498843476
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- from: 2
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to: 4
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count: 96
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probability: 8.385685634621701e-6
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- from: 3
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to: 0
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count: 193315
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probability: 0.9743748708410829
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- from: 3
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to: 1
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count: 4270
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probability: 0.021522285898618442
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- from: 3
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to: 2
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count: 690
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probability: 0.0034778401100812
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- from: 3
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to: 3
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count: 98
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probability: 0.0004939541025912429
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- from: 3
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to: 4
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count: 26
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probability: 0.0001310490476262481
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- from: 4
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to: 0
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count: 23125
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probability: 0.9846291407647109
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- from: 4
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to: 1
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count: 225
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probability: 0.009580175423656646
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- from: 4
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to: 2
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count: 96
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probability: 0.004087541514093502
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- from: 4
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to: 3
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count: 26
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probability: 0.0011070424934003236
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- from: 4
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to: 4
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count: 14
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probability: 0.0005960998041386358
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composition_transitions:
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- from: 'A'
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to: 'A'
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count: 162260
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probability: 0.47062167539692207
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- from: 'A'
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to: 'C'
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count: 27810
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cost: 2.5439415226130238
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- pair: A/G
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probability: 0.08066059899413536
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- from: 'A'
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to: 'G'
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count: 130153
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cost: 1.0
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- pair: A/T
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probability: 0.3774979842101294
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- from: 'A'
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to: 'T'
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count: 24555
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cost: 2.6684722241428322
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- pair: C/G
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probability: 0.07121974139881315
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- from: 'C'
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to: 'A'
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count: 27810
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probability: 0.07790832534920075
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- from: 'C'
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to: 'C'
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count: 184633
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probability: 0.5172401234879174
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- from: 'C'
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to: 'G'
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count: 19637
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cost: 2.892062911764701
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- pair: C/T
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probability: 0.05501207424963161
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- from: 'C'
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to: 'T'
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count: 124878
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cost: 1.0413902163542994
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- pair: G/T
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probability: 0.3498394769132503
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- from: 'G'
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to: 'A'
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count: 130153
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probability: 0.36057158212891627
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- from: 'G'
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to: 'C'
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count: 19637
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probability: 0.054401697680925745
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- from: 'G'
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to: 'G'
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count: 184557
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probability: 0.5112906308956874
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- from: 'G'
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to: 'T'
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count: 26616
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cost: 2.5878424665170052
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probability: 0.07373608929447062
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- from: 'T'
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to: 'A'
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count: 24555
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probability: 0.07337692220342934
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- from: 'T'
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to: 'C'
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count: 124878
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probability: 0.3731689387464813
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- from: 'T'
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to: 'G'
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count: 26616
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probability: 0.07953574267426085
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- from: 'T'
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to: 'T'
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count: 158593
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probability: 0.4739183963758285
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