Eric Coissac
eee71430a4
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
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: 54999793
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probability: 0.7934021725308564
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- from: 0
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to: 1
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count: 8873859
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probability: 0.12801028195383377
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- from: 0
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to: 2
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count: 5305545
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probability: 0.07653539585976665
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- from: 0
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to: 3
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count: 126109
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probability: 0.001819191475424167
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- from: 0
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to: 4
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count: 16149
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probability: 0.00023295818011898336
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- from: 1
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to: 0
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count: 8873859
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probability: 0.8510749571674425
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- from: 1
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to: 1
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count: 1041044
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probability: 0.09984455215137214
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- from: 1
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to: 2
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count: 507272
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probability: 0.048651493749477304
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- from: 1
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to: 3
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count: 4248
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probability: 0.00040741760918753563
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- from: 1
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to: 4
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count: 225
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probability: 0.00002157932252052625
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- from: 2
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to: 0
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count: 5305545
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probability: 0.9117891245815953
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- from: 2
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to: 1
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count: 507272
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probability: 0.08717767784549091
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- from: 2
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to: 2
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count: 5227
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probability: 0.0008982907041949506
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- from: 2
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to: 3
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count: 689
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probability: 0.00011840870388182915
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- from: 2
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to: 4
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count: 96
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probability: 0.000016498164836945715
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- from: 3
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to: 0
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count: 126109
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probability: 0.9614164824273843
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- from: 3
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to: 1
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count: 4248
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probability: 0.03238545399100404
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- from: 3
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to: 2
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count: 689
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probability: 0.005252725470763132
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- from: 3
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to: 3
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count: 98
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probability: 0.0007471220553480217
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- from: 3
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to: 4
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count: 26
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probability: 0.00019821605550049553
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- from: 4
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to: 0
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count: 16149
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probability: 0.9781344639612356
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- from: 4
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to: 1
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count: 225
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probability: 0.013628104179285281
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- from: 4
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to: 2
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count: 96
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probability: 0.00581465778316172
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- from: 4
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to: 3
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count: 26
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probability: 0.0015748031496062992
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- from: 4
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to: 4
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count: 14
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probability: 0.0008479709267110841
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composition_transitions:
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- from: 'A'
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to: 'A'
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count: 161774
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probability: 0.4701762136303263
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- from: 'A'
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to: 'C'
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count: 27788
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probability: 0.0807624007835592
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- from: 'A'
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to: 'G'
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count: 130019
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probability: 0.3778842157577942
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- from: 'A'
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to: 'T'
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count: 24490
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probability: 0.07117716982832031
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- from: 'C'
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to: 'A'
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count: 27788
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probability: 0.0780165140757087
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- from: 'C'
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to: 'C'
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count: 184047
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probability: 0.5167232390273484
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- from: 'C'
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to: 'G'
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count: 19622
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probability: 0.05508996830263265
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- from: 'C'
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to: 'T'
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count: 124724
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probability: 0.3501702785943102
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- from: 'G'
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to: 'A'
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count: 130019
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probability: 0.3610094570655886
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- from: 'G'
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to: 'C'
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count: 19622
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probability: 0.05448224926003876
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- from: 'G'
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to: 'G'
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count: 183951
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probability: 0.5107565097152884
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- from: 'G'
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to: 'T'
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count: 26562
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probability: 0.07375178395908417
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- from: 'T'
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to: 'A'
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count: 24490
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probability: 0.07335783586895636
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- from: 'T'
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to: 'C'
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count: 124724
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probability: 0.37360076443118473
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- from: 'T'
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to: 'G'
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count: 26562
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probability: 0.07956434611479049
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- from: 'T'
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to: 'T'
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count: 158067
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probability: 0.4734770535850684
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