add name-tree command and fix --free-loss cost matrix

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.

sankoff_params.yaml

@@ -2,166 +2,166 @@ ratio_ceiling: 0.5
 cardinality_transitions:
 - from: 0
   to: 0
-  count: 37622567
-  probability: 0.7765461217831444
+  count: 54999793
+  probability: 0.7934021725308564
 - from: 0
   to: 1
-  count: 6977400
-  probability: 0.14401656617768033
+  count: 8873859
+  probability: 0.12801028195383377
 - from: 0
   to: 2
-  count: 3744558
-  probability: 0.0772893033240408
+  count: 5305545
+  probability: 0.07653539585976665
 - from: 0
   to: 3
-  count: 91083
-  probability: 0.0018799926759482985
+  count: 126109
+  probability: 0.001819191475424167
 - from: 0
   to: 4
-  count: 12985
-  probability: 0.0002680160391861122
+  count: 16149
+  probability: 0.00023295818011898336
 - from: 1
   to: 0
-  count: 6977400
-  probability: 0.820630384894398
+  count: 8873859
+  probability: 0.8510749571674425
 - from: 1
   to: 1
-  count: 1018042
-  probability: 0.1197346000370715
+  count: 1041044
+  probability: 0.09984455215137214
 - from: 1
   to: 2
-  count: 502624
-  probability: 0.05911493200578466
+  count: 507272
+  probability: 0.048651493749477304
 - from: 1
   to: 3
-  count: 4197
-  probability: 0.000493620220340211
+  count: 4248
+  probability: 0.00040741760918753563
 - from: 1
   to: 4
   count: 225
-  probability: 0.000026462842405658202
+  probability: 0.00002157932252052625
 - from: 2
   to: 0
-  count: 3744558
-  probability: 0.8804244781723005
+  count: 5305545
+  probability: 0.9117891245815953
 - from: 2
   to: 1
-  count: 502624
-  probability: 0.11817749195415704
+  count: 507272
+  probability: 0.08717767784549091
 - from: 2
   to: 2
-  count: 5162
-  probability: 0.0012136949558066439
+  count: 5227
+  probability: 0.0008982907041949506
 - from: 2
   to: 3
-  count: 688
-  probability: 0.0001617632951559417
+  count: 689
+  probability: 0.00011840870388182915
 - from: 2
   to: 4
   count: 96
-  probability: 0.00002257162257989884
+  probability: 0.000016498164836945715
 - from: 3
   to: 0
-  count: 91083
-  probability: 0.9478728718311618
+  count: 126109
+  probability: 0.9614164824273843
 - from: 3
   to: 1
-  count: 4197
-  probability: 0.04367689297756317
+  count: 4248
+  probability: 0.03238545399100404
 - from: 3
   to: 2
-  count: 688
-  probability: 0.007159805186696083
+  count: 689
+  probability: 0.005252725470763132
 - from: 3
   to: 3
   count: 98
-  probability: 0.0010198559713607792
+  probability: 0.0007471220553480217
 - from: 3
   to: 4
   count: 26
-  probability: 0.00027057403321816594
+  probability: 0.00019821605550049553
 - from: 4
   to: 0
-  count: 12985
-  probability: 0.972950696838004
+  count: 16149
+  probability: 0.9781344639612356
 - from: 4
   to: 1
   count: 225
-  probability: 0.01685898396523303
+  probability: 0.013628104179285281
 - from: 4
   to: 2
   count: 96
-  probability: 0.0071931664918327585
+  probability: 0.00581465778316172
 - from: 4
   to: 3
   count: 26
-  probability: 0.0019481492582047056
+  probability: 0.0015748031496062992
 - from: 4
   to: 4
   count: 14
-  probability: 0.0010490034467256107
+  probability: 0.0008479709267110841
 composition_transitions:
 - from: 'A'
   to: 'A'
-  count: 157182
-  probability: 0.46648741052031767
+  count: 161774
+  probability: 0.4701762136303263
 - from: 'A'
   to: 'C'
-  count: 27305
-  probability: 0.08103624298111281
+  count: 27788
+  probability: 0.0807624007835592
 - from: 'A'
   to: 'G'
-  count: 128548
-  probability: 0.38150693875612857
+  count: 130019
+  probability: 0.3778842157577942
 - from: 'A'
   to: 'T'
-  count: 23913
-  probability: 0.07096940774244097
+  count: 24490
+  probability: 0.07117716982832031
 - from: 'C'
   to: 'A'
-  count: 27305
-  probability: 0.07823849488677553
+  count: 27788
+  probability: 0.0780165140757087
 - from: 'C'
   to: 'C'
-  count: 179118
-  probability: 0.5132365034656459
+  count: 184047
+  probability: 0.5167232390273484
 - from: 'C'
   to: 'G'
-  count: 19392
-  probability: 0.055564947549692406
+  count: 19622
+  probability: 0.05508996830263265
 - from: 'C'
   to: 'T'
-  count: 123182
-  probability: 0.3529600540978862
+  count: 124724
+  probability: 0.3501702785943102
 - from: 'G'
   to: 'A'
-  count: 128548
-  probability: 0.3637269077214298
+  count: 130019
+  probability: 0.3610094570655886
 - from: 'G'
   to: 'C'
-  count: 19392
-  probability: 0.05486971555009776
+  count: 19622
+  probability: 0.05448224926003876
 - from: 'G'
   to: 'G'
-  count: 179245
-  probability: 0.5071742039901647
+  count: 183951
+  probability: 0.5107565097152884
 - from: 'G'
   to: 'T'
-  count: 26234
-  probability: 0.07422917273830779
+  count: 26562
+  probability: 0.07375178395908417
 - from: 'T'
   to: 'A'
-  count: 23913
-  probability: 0.07307212790143376
+  count: 24490
+  probability: 0.07335783586895636
 - from: 'T'
   to: 'C'
-  count: 123182
-  probability: 0.3764132839524281
+  count: 124724
+  probability: 0.37360076443118473
 - from: 'T'
   to: 'G'
-  count: 26234
-  probability: 0.08016452153080807
+  count: 26562
+  probability: 0.07956434611479049
 - from: 'T'
   to: 'T'
-  count: 153923
-  probability: 0.4703500666153301
+  count: 158067
+  probability: 0.4734770535850684