Eric Coissac
8615da59a8
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.
168 lines
2.9 KiB
YAML
168 lines
2.9 KiB
YAML
ratio_ceiling: 0.5
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cardinality_transitions:
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- from: 0
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to: 0
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count: 37622567
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probability: 0.7765461217831444
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- from: 0
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to: 1
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count: 6977400
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probability: 0.14401656617768033
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- from: 0
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to: 2
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count: 3744558
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probability: 0.0772893033240408
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- from: 0
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to: 3
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count: 91083
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probability: 0.0018799926759482985
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- from: 0
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to: 4
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count: 12985
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probability: 0.0002680160391861122
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- from: 1
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to: 0
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count: 6977400
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probability: 0.820630384894398
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- from: 1
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to: 1
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count: 1018042
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probability: 0.1197346000370715
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- from: 1
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to: 2
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count: 502624
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probability: 0.05911493200578466
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- from: 1
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to: 3
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count: 4197
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probability: 0.000493620220340211
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- from: 1
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to: 4
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count: 225
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probability: 0.000026462842405658202
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- from: 2
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to: 0
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count: 3744558
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probability: 0.8804244781723005
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- from: 2
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to: 1
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count: 502624
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probability: 0.11817749195415704
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- from: 2
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to: 2
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count: 5162
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probability: 0.0012136949558066439
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- from: 2
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to: 3
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count: 688
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probability: 0.0001617632951559417
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- from: 2
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to: 4
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count: 96
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probability: 0.00002257162257989884
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- from: 3
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to: 0
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count: 91083
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probability: 0.9478728718311618
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- from: 3
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to: 1
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count: 4197
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probability: 0.04367689297756317
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- from: 3
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to: 2
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count: 688
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probability: 0.007159805186696083
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- from: 3
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to: 3
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count: 98
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probability: 0.0010198559713607792
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- from: 3
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to: 4
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count: 26
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probability: 0.00027057403321816594
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- from: 4
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to: 0
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count: 12985
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probability: 0.972950696838004
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- from: 4
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to: 1
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count: 225
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probability: 0.01685898396523303
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- from: 4
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to: 2
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count: 96
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probability: 0.0071931664918327585
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- from: 4
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to: 3
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count: 26
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probability: 0.0019481492582047056
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- from: 4
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to: 4
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count: 14
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probability: 0.0010490034467256107
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composition_transitions:
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- from: 'A'
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to: 'A'
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count: 157182
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probability: 0.46648741052031767
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- from: 'A'
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to: 'C'
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count: 27305
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probability: 0.08103624298111281
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- from: 'A'
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to: 'G'
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count: 128548
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probability: 0.38150693875612857
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- from: 'A'
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to: 'T'
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count: 23913
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probability: 0.07096940774244097
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- from: 'C'
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to: 'A'
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count: 27305
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probability: 0.07823849488677553
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- from: 'C'
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to: 'C'
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count: 179118
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probability: 0.5132365034656459
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- from: 'C'
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to: 'G'
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count: 19392
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probability: 0.055564947549692406
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- from: 'C'
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to: 'T'
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count: 123182
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probability: 0.3529600540978862
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- from: 'G'
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to: 'A'
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count: 128548
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probability: 0.3637269077214298
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- from: 'G'
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to: 'C'
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count: 19392
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probability: 0.05486971555009776
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- from: 'G'
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to: 'G'
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count: 179245
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probability: 0.5071742039901647
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- from: 'G'
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to: 'T'
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count: 26234
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probability: 0.07422917273830779
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- from: 'T'
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to: 'A'
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count: 23913
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probability: 0.07307212790143376
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- from: 'T'
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to: 'C'
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count: 123182
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probability: 0.3764132839524281
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- from: 'T'
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to: 'G'
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count: 26234
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probability: 0.08016452153080807
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- from: 'T'
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to: 'T'
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count: 153923
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probability: 0.4703500666153301
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