Athanasius Ultrametric

Reports / homoplasy_analysis.md

Homoplasy and Recurrent States

Generated by scripts/run_homoplasy_analysis.py.

A candidate recurrent state is an encoded feature-state that appears in more than one disconnected pure region of the consensus tree and whose feature requires more parsimony changes than the theoretical minimum. Minority recurrent states are the more plausible repeated-innovation candidates, but even these identify possible repeated correction, parallel change, reversal, contamination, or coding artefact; they do not prove direction of change.

Outputs

Summary

dataset features homoplastic_features homoplastic_feature_fraction mean_parsimony_score mean_excess_changes candidate_recurrent_states candidate_recurrent_minority_states max_state_component_count
athanasius_epistles_data_bin_csv 36 31 0.861111 2.47222 1.47222 62 37 6
athanasius_epistles_data_multistate_csv 30 23 0.766667 2.96667 1.2 49 32 6

Top Candidate Recurrent States

dataset feature state state_witnesses state_size state_fraction minority_state component_count component_nodes component_members feature_state_count feature_parsimony_score feature_minimum_possible_changes feature_excess_changes candidate_recurrent_state candidate_recurrent_minority_state
athanasius_epistles_data_bin_csv 1Cor.2.4.1.b1 0 A Ath C M1739 M223 M2423 6 0.5 1 5 A; C; M1739; Ath; N4 A; C; M1739; Ath; M223 M2423 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b1 0 A Ath F G M1739 P46 6 0.5 1 5 P46; A; M1739; Ath; N2 P46; A; M1739; Ath; F G 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor.9.22.1.b2 0 A Ath B M1739 P46 U1 6 0.5 1 5 P46; A; B; N3; Ath P46; A; B; M1739 U1; Ath 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 1Cor.2.4.1.b1 1 B D F G P46 U1 6 0.5 1 4 P46; B; U1; N5 P46; B; U1; D F G 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b1 1 B C D M223 M2423 U1 6 0.5 1 4 N1; U1; N4; D B C; U1; M223 M2423; D 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b2 0 Ath F G M1739 P46 U1 6 0.5 1 4 P46; N3; Ath; N2 P46; M1739 U1; Ath; F G 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b2 1 A B C D M223 M2423 6 0.5 1 4 A; N1; N4; D A; B C; M223 M2423; D 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor.2.4.1.b2 0 Ath F G M223 P46 5 0.416667 1 4 P46; Ath; M223; N2 P46; Ath; M223; F G 2 4 1 3 1 1
athanasius_epistles_data_bin_csv Phil.2.5.1 0 A Ath B C U1 5 0.416667 1 4 A; N1; U1; Ath A; B C; U1; Ath 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor.15.53.1.b1 0 Ath F P46 U1 4 0.333333 1 4 P46; U1; Ath; F P46; U1; Ath; F 2 4 1 3 1 1
athanasius_epistles_data_bin_csv 1Cor.15.55.1.b2 0 Ath B C M1739 P46 U1 6 0.5 1 4 P46; N1; N3; Ath P46; B C; M1739 U1; Ath 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Col.1.16.1.b2 0 A Ath B C M223 M2423 6 0.5 1 4 A; N1; Ath; N4 A; B C; Ath; M223 M2423 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Phil.2.9.1 1 A C M1739 P46 U1 5 0.416667 1 4 P46; A; C; N3 P46; A; C; M1739 U1 2 2 1 1 1 1
athanasius_epistles_data_bin_csv 1Cor.15.55.1.b2 1 A D F G M223 M2423 6 0.5 1 3 A; N4; N5 A; M223 M2423; D F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 1Cor.9.22.1.b2 1 C D F G M223 M2423 6 0.5 1 3 C; N4; N5 C; M223 M2423; D F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Col.1.16.1.b2 1 D F G M1739 P46 U1 6 0.5 1 3 P46; N3; N5 P46; M1739 U1; D F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 2Cor.1.10.1.b2 1 F G M1739 M223 M2423 5 0.416667 1 3 M1739; N4; N2 M1739; M223 M2423; F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Eph.3.18.1 1 A M1739 M223 M2423 U1 5 0.416667 1 3 A; N3; N4 A; M1739 U1; M223 M2423 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 1Cor.15.55.1.b1 0 A Ath M223 M2423 4 0.333333 1 3 A; Ath; N4 A; Ath; M223 M2423 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 1Cor.4.6.3.b1 0 Ath F G M2423 4 0.333333 1 3 Ath; M2423; N2 Ath; M2423; F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Col.1.16.1.b1 1 A B M223 M2423 4 0.333333 1 3 A; B; N4 A; B; M223 M2423 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Rom.8.22.1 1 B F G P46 4 0.333333 1 3 P46; B; N2 P46; B; F G 2 3 1 2 1 1
athanasius_epistles_data_bin_csv Col.1.18.2 1 B M1739 P46 3 0.25 1 3 P46; B; M1739 P46; B; M1739 2 3 1 2 1 1
athanasius_epistles_data_bin_csv 1Cor.11.2.1 1 D F G M223 M2423 5 0.416667 1 2 N4; N5 M223 M2423; D F G 2 2 1 1 1 1
athanasius_epistles_data_bin_csv 1Cor.9.16.2 1 B C D F G 5 0.416667 1 2 N1; N5 B C; D F G 2 2 1 1 1 1
athanasius_epistles_data_bin_csv 1Cor.11.2.2.b2 1 C D F G 4 0.333333 1 2 C; N5 C; D F G 2 2 1 1 1 1
athanasius_epistles_data_bin_csv 1Cor.4.6.3.b3 1 F G M223 M2423 4 0.333333 1 2 N4; N2 M223 M2423; F G 2 2 1 1 1 1
athanasius_epistles_data_bin_csv Rom.15.19.1.b1 0 Ath D F G 4 0.333333 1 2 Ath; N5 Ath; D F G 2 2 1 1 1 1
athanasius_epistles_data_bin_csv 1Cor.15.47.1.b2 1 A M223 M2423 3 0.25 1 2 A; N4 A; M223 M2423 2 2 1 1 1 1
athanasius_epistles_data_bin_csv Col.1.16.2 1 M1739 P46 U1 3 0.25 1 2 P46; N3 P46; M1739 U1 2 2 1 1 1 1

Most Homoplastic Features

dataset feature state_count parsimony_score minimum_possible_changes excess_changes consistency_index homoplastic_feature
athanasius_epistles_data_bin_csv 1Cor.15.53.1.b1 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv 1Cor.2.4.1.b1 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv 1Cor.2.4.1.b2 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b1 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv 1Cor15.54.1.b2 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv Phil.2.5.1 2 4 1 3 0.25 1
athanasius_epistles_data_bin_csv 1Cor.15.55.1.b1 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv 1Cor.15.55.1.b2 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv 1Cor.4.6.3.b1 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv 1Cor.9.22.1.b2 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv 2Cor.1.10.1.b2 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv Col.1.16.1.b1 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv Col.1.16.1.b2 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv Col.1.18.2 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv Eph.3.18.1 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv Rom.8.22.1 2 3 1 2 0.333333 1
athanasius_epistles_data_bin_csv 1Cor.1.24.1 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.11.2.1 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.11.2.2.b2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.15.47.1.b2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.4.6.3.b2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.4.6.3.b3 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 1Cor.9.16.2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv 2Cor.1.10.1.b1 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Col.1.16.2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Col.1.18.3 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Eph.3.19.2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Phil.2.5.2 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Phil.2.6.1 2 2 1 1 0.5 1
athanasius_epistles_data_bin_csv Phil.2.9.1 2 2 1 1 0.5 1