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Weak and alignment-sensitive branches must remain flagged.","No justified outgroup is available in the structure-selected sample. Tree is unrooted; rectangular/circular layouts use an arbitrary traversal origin and do not imply direction or time.","Comparison intervals combine deposited constructs, published structure-assisted alignments, curated CDD model spans and explicitly marked homolog transfers. They are not uniformly experimentally certified isolated folds.","Nine nonhuman comparators are sparse and selected for structure availability; Jasper and the trypanosome entry are UniProt-unreviewed but experimentally sequence-mapped. No universal family census or species phylogeny is claimed.","Conservation is unweighted Shannon entropy in this sampled alignment. It does not establish binding, histone specificity, pocket equivalence, chemical selectivity or therapeutic interchangeability.","Human HDGF and rat Hdgf have identical retained sequences; their divergence and internal order cannot be inferred. The pdp2 composition test flags an uncorrected p\u22480.0136 among39 sequences; this is a model diagnostic, not proof of compositional bias.","Three predicted PWWP-like human candidates are displayed separately and excluded from alignment/tree.","Source-deposited engineered substitutions are not substituted into the canonical sequences used for inference. Coordinate-contact observations are not affinity measurements."],"metadata":{"alignment_length":257,"analysis_id":"PWWP-EVO-1.0.0","analysis_kind":"maximum_likelihood_domain_phylogeny","branch_length_units":"expected amino-acid substitutions per retained alignment site","candidate_count":3,"dataset_version":"v1.2 frozen source; independently derived evolution1.0.0","date":"2026-10-26","display_policy":"Support-qualified unrooted inference; low-support and sensitivity-dependent branching remains unresolved.","domain_count":39,"excluded_columns":179,"identical_retained_sequence_groups":[["P51858_PWWP1","Q8VHK7_PWWP1"]],"input_source_sha256":{"core_residue_correspondence.csv":"7bd79cc827b90bf631588f96ef3125cc778e3435202dddc1adea59c93267a384","domains.csv":"27e4f350f4c5dc82912bb695c1f26f27840d10fe1237e47c6667d5040b0b1149","proteins.csv":"d9143412b2fd4382cf4fa2549cc07d4bd0dd73be101f4b9d3877fb4e12a6e02d","pwwp_atlas_public_v1.2.sqlite":"0c53107a39e222b48611302b21fda5fb4ed50b190b6b39d41423ccc5ca5958f6"},"model":"LG+G4","provisional":false,"retained_columns":78,"rooting":"Unrooted. Arbitrary three-way display traversal origin only; no ancestral or time interpretation.","sampling_scope":"Human-centered curated Atlas domain set plus nine structural comparators; no additional taxa.","seed":20261026,"sensitivity_seed":20261027,"software":{"Biopython":"1.88","IQ-TREE":"2.4.0 Linux x86_64 built Feb7 2025","MAFFT":"7.526 (2024/Apr/26)"},"statistics":{"internal_branches":36,"maximum_rf_for_bifurcating_trees":72,"note":"An identical split in the sensitivity tree is a stability check, not independent replication.","primary_supported_branches":13,"primary_weak_branches":23,"robinson_foulds_distance":0,"robust_branches_both_masks":12,"shared_unrooted_splits":36,"supported_and_recovered_in_sensitivity":13},"status":"exploratory_unrooted_phylogeny","support":{"bnni":true,"reporting_thresholds":{"sh_alrt":80,"ufboot":95},"sh_alrt_replicates":1000,"ufboot_replicates":1000},"supported_tree_policy":"Cladogram retaining only splits meeting SH-aLRT80 and UFBoot95 in both primary and broader masks; unsupported edges are contracted. No evolutionary length scale in this view.","title":"PWWP domain relationships","version":"1.0.0"},"newick":"(P29374_PWWP1:1.0635223602,Q4LE39_PWWP1:0.0140052014,((((O95696_PWWP1:0.2264658398,Q9ULD4_PWWP1:0.1388776833)28/64:0.0391966965,P55201_PWWP1:0.2068983906)99.7/100:1.4003885110,(((((((Q9Y6K1_PWWP1:0.2486136850,(Q9UBC3_PWWP1:0.0000025823,O88509_PWWP1:0.0346957180)97.6/100:0.4268002584)91.7/69:0.5123901198,(Q96N64_PWWP1:0.3853992098,Q6NUJ5_PWWP1:0.0617308128)96.3/99:0.9033280004)64.1/62:0.5346738500,Q9P267_PWWP1:1.2146930238)82.3/50:0.3906822151,((Q49A26_PWWP1:0.7784958054,(((P51858_PWWP1:0.0000010000,Q8VHK7_PWWP1:0.0000010000)0/100:0.0000022991,(Q5TGJ6_PWWP1:0.2586620956,((Q7Z4V5_PWWP1:0.1304455355,O75475_PWWP1:0.1612071778)91.9/96:0.0981943195,(Q9Y3E1_PWWP1:0.0000010000,Q9JMG7_PWWP1:0.0000010000)74.4/98:0.0192236365)92.1/97:0.1325531540)82.9/82:0.0442354467)99.3/97:0.8309548879,Q9VAA9_PWWP1:0.2669051033)92.9/93:0.4360820842)75.6/65:0.2625303924,((Q96L73_PWWP2:0.1545860858,O96028_PWWP2:0.1875321951)86.7/95:0.1602084862,Q9BZ95_PWWP2:0.0152173772)99.8/100:1.7157268270)0/16:0.0471681552)24.7/15:0.1235380074,((Q15326_PWWP1:0.0000028522,Q8R5C8_PWWP1:0.0135763277)89.1/99:0.4678908745,Q9ULU4_PWWP1:0.7563368901)99.5/100:1.1059805370)77/41:0.1482980958,(((Q2TAK8_PWWP1:0.3658932928,Q5H9M0_PWWP1:0.1399639110)67.9/83:0.1466262746,A0A494C071_PWWP1:0.3435006546)100/100:2.0452561750,((Q9H0M4_PWWP1:0.9744708409,Q586Y0_PWWP1:1.7568776336)44.1/32:0.1243735060,Q504Y3_PWWP1:1.8185080526)73.6/32:0.1764445632)71.7/34:0.1959264517)72.1/30:0.1269719470,(P52701_PWWP1:0.8091295885,((Q96L73_PWWP1:0.7699145845,O96028_PWWP1:0.1760001724)75.3/71:0.1567025951,Q9BZ95_PWWP1:0.3507408622)97.1/99:0.6252460866)77.7/52:0.1708604459)86.4/71:0.3144622501)77.3/60:0.2302031452,((O59676_PWWP1:1.2012976942,O94312_PWWP1:0.7558833699)87.9/92:0.4439253286,Q04213_PWWP1:0.9244668427)72.9/72:0.2807254496)99.8/100:1.8369594180);","newick_supported":"(P29374_PWWP1,Q4LE39_PWWP1,((O95696_PWWP1,Q9ULD4_PWWP1,P55201_PWWP1)99.7/100,Q9Y6K1_PWWP1,(Q9UBC3_PWWP1,O88509_PWWP1)97.6/100,(Q96N64_PWWP1,Q6NUJ5_PWWP1)96.3/99,Q9P267_PWWP1,Q49A26_PWWP1,(P51858_PWWP1,Q8VHK7_PWWP1,Q5TGJ6_PWWP1,((Q7Z4V5_PWWP1,O75475_PWWP1)91.9/96,Q9Y3E1_PWWP1,Q9JMG7_PWWP1)92.1/97)99.3/97,Q9VAA9_PWWP1,(Q96L73_PWWP2,O96028_PWWP2,Q9BZ95_PWWP2)99.8/100,((Q15326_PWWP1,Q8R5C8_PWWP1)89.1/99,Q9ULU4_PWWP1)99.5/100,(Q2TAK8_PWWP1,Q5H9M0_PWWP1,A0A494C071_PWWP1)100/100,Q9H0M4_PWWP1,Q586Y0_PWWP1,Q504Y3_PWWP1,P52701_PWWP1,(Q96L73_PWWP1,O96028_PWWP1,Q9BZ95_PWWP1)97.1/99,O59676_PWWP1,O94312_PWWP1,Q04213_PWWP1)99.8/100);","phase5_diagnostics":{"analysis_id":"PWWP-EVO-DIAGNOSTICS-5.0.0","architecture":{"canonical_proteins":39,"other_source_features":71,"rule":"Absolute scale uses canonical amino-acid positions; normalized scale divides each interval by its own protein length. No coordinate projection onto unvalidated isoforms.","selected_constructs":46,"validated_isoform_domain_correspondences":103},"composition_flags":[{"leaf_id":"O94312_PWWP1","reported_p_value":0.0136,"scope":"Uncorrected per-sequence composition chi-square diagnostic from the original IQ-TREE log, 39 tested sequences. Not a standalone model-adequacy rejection."}],"decisions":["Retain all 39 original domain instances and the unrooted support-collapsed default. The 78-site primary alignment resolves selected local splits; deep relationships remain unresolved.","Thirty human domain instances and nine structural comparators across six nonhuman species are uneven family sampling. Existing comparators are not a family-wide orthology panel or a defensible outgroup.","Boundary evidence remains heterogeneous: 24 deposited domain constructs, eight published structure-assisted intervals, three homology-mapped intervals, three CDD homology intervals and one structure-supported subdomain. The original source-specific qualifications remain attached.","The 108-site alternative mask recovers the same 36 best-tree splits, but only 12 pass both support thresholds in both analyses. Mask agreement is sensitivity evidence, not independent replication.","Four pairs have at least 95% identity over at least 60 paired nongap retained positions. Preserve all tips; identical paired residues with different gap patterns are not identical complete alignment strings.","The pdp2 composition flag has an uncorrected reported p value of 0.0136 among 39 sequences. This flag motivates assessment in a future balanced analysis; it does not by itself establish model failure.","No new phylogeny is promoted. Balanced subgroup-specific homolog selection, independently supported folded boundaries and model adequacy tests need a separately versioned sequence set and full inference/support pipeline; graphical branch operations cannot answer those biological questions.","Subtree conservation is descriptive unweighted 1 minus Shannon entropy divided by ln(20), excluding gaps and displaying occupancy separately. Original inference inclusion/exclusion decisions are unchanged by subgroup selection."],"future_sampling_protocol":["Select a predeclared set of taxa spanning each supported human subgroup, then verify PWWP-domain homolog boundaries with UniProt/InterPro plus available deposited constructs.","Record orthology/paralogy uncertainty and preserve PWWP1/PWWP2 as independent instances; do not select sequences to improve bootstrap values.","Qualify alternative alignments, column masks, composition, informative sites and saturation before fitting models. Retain sequence-near-duplicate diagnostics without silently deleting tips.","Compare unrooted split robustness under boundary, taxon and mask changes. Root or date the tree only with an independently justified biological model."],"inference":{"formal_model_adequacy":"Not established by model selection or support alone. No new posterior-predictive or parametric adequacy test executed.","full_alignment_columns":257,"model":"LG+G4","primary_internal_splits":36,"primary_sites":78,"robust_splits":12,"rooting":"Unrooted. Arbitrary three-way display traversal origin only; no ancestral or time interpretation.","sensitivity_sites":108,"shared_primary_sensitivity_splits":36},"near_identical_pairs":[{"complete_retained_strings_identical":false,"domain_A":"UP:Q9UBC3:PWWP1","domain_B":"UP:O88509:PWWP1","identical_amino_acids":75,"paired_identity":0.961538462,"paired_nongap_positions":78,"scope":"Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction."},{"complete_retained_strings_identical":true,"domain_A":"UP:P51858:PWWP1","domain_B":"UP:Q8VHK7:PWWP1","identical_amino_acids":77,"paired_identity":1.0,"paired_nongap_positions":77,"scope":"Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction."},{"complete_retained_strings_identical":false,"domain_A":"UP:Q9Y3E1:PWWP1","domain_B":"UP:Q9JMG7:PWWP1","identical_amino_acids":74,"paired_identity":1.0,"paired_nongap_positions":74,"scope":"Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction."},{"complete_retained_strings_identical":false,"domain_A":"UP:Q15326:PWWP1","domain_B":"UP:Q8R5C8:PWWP1","identical_amino_acids":71,"paired_identity":0.986111111,"paired_nongap_positions":72,"scope":"Descriptive identity among mutually observed retained sites. Not an evolutionary distance or a pharmacology prediction."}],"release_date":"2026-10-26","sample":{"boundary_methods":{"CDD_homology_model":3,"experimentally_deposited_domain_construct":24,"homology_mapped_construct":3,"published_structure_assisted_alignment":8,"structure_supported_subdomain":1},"domain_instances":39,"human_domain_instances":30,"nonhuman_domain_instances":9,"species_count":7,"species_counts":{"Drosophila melanogaster":1,"Homo sapiens":30,"Mus musculus":3,"Rattus norvegicus":1,"Saccharomyces cerevisiae (strain ATCC 204508 / S288c)":1,"Schizosaccharomyces pombe (strain 972 / ATCC 24843)":2,"Trypanosoma brucei brucei (strain 927/4 GUTat10.1)":1}},"source_analysis_id":"PWWP-EVO-1.0.0","source_sha256":{"analysis/discovery_v1/atlas_discovery.json":"bd55b3a156b57e1c1fb1b6a477fbf4c000f6ef9e35a5446409caf38a7579d8de","analysis/evolution_v1/alignment_masked.fasta":"339896b0952c2b12aef91f28d56f844a385a1ca8277bf18d11237079b7ac8840","analysis/evolution_v1/atlas_evolution.json":"43207bd7947d128636d2a2a439cb427fb08afbe2551dc701cdfa0aa9a5a3e9f2","analysis/evolution_v1/logs/iqtree_primary.stdout.log":"bde170b594bc6b5cfb135c2da0b34f29552e5d944eb86151a4b5172cf621376c","analysis/evolution_v1/trees/primary.iqtree":"4b0e1832ffead87c9b415de06a67e54f0365119d9123b273ebbbe0945eb5f5b4","analysis/evolution_v1/trees/sensitivity50.iqtree":"11f273c0e20f7694d7e883f8be593f7cb84a13f9b06a2564b26b49da9d162c85"},"visualization_reference":{"authors":"Storm CE; Sonnhammer ELL","doi":"10.1093/bioinformatics/17.4.343","pmid":"11301303","retrieved_date":"2026-10-26","title":"NIFAS: visual analysis of domain evolution in proteins","url":"https://pubmed.ncbi.nlm.nih.gov/11301303/","verification_scope":"Primary bibliographic record and abstract; linked tree/domain architecture concept only. No code, layout or figure copied.","year":2001}},"published_comparison":[{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Recovered with both primary support thresholds; compare sensitivity before interpretation.","primary_recovered":true,"primary_support":{"sh_alrt":99.7,"ufboot":100.0},"published_description":"BRPF1, BRPF2/BRD1 and BRPF3 subgroup","reference_doi":"10.1186/1471-2148-12-101","relationship":"BRPF subgroup","sensitivity_recovered":true,"sensitivity_support":{"sh_alrt":99.9,"ufboot":100.0},"tested_leaves":["O95696_PWWP1","P55201_PWWP1","Q9ULD4_PWWP1"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Recovered with both primary support thresholds; compare sensitivity before interpretation.","primary_recovered":true,"primary_support":{"sh_alrt":99.8,"ufboot":100.0},"published_description":"The b/C-terminal NSD domains form a subgroup distinct from a/N-terminal domains","reference_doi":"10.1186/1471-2148-12-101","relationship":"NSD second PWWP domains","sensitivity_recovered":true,"sensitivity_support":{"sh_alrt":100.0,"ufboot":100.0},"tested_leaves":["O96028_PWWP2","Q96L73_PWWP2","Q9BZ95_PWWP2"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Recovered with both primary support thresholds; compare sensitivity before interpretation.","primary_recovered":true,"primary_support":{"sh_alrt":97.1,"ufboot":99.0},"published_description":"NSD a/N-terminal domains; published broader group includes MSH6","reference_doi":"10.1186/1471-2148-12-101","relationship":"NSD first PWWP domains","sensitivity_recovered":true,"sensitivity_support":{"sh_alrt":98.3,"ufboot":99.0},"tested_leaves":["O96028_PWWP1","Q96L73_PWWP1","Q9BZ95_PWWP1"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Present in best tree but below one or both support thresholds; unresolved.","primary_recovered":true,"primary_support":{"sh_alrt":77.7,"ufboot":52.0},"published_description":"Published a-type grouping with MSH6","reference_doi":"10.1186/1471-2148-12-101","relationship":"NSD first domains plus MSH6","sensitivity_recovered":true,"sensitivity_support":{"sh_alrt":84.0,"ufboot":47.0},"tested_leaves":["O96028_PWWP1","P52701_PWWP1","Q96L73_PWWP1","Q9BZ95_PWWP1"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Exact sampled split not recovered; this short differently sampled analysis does not establish a contradiction of the published history.","primary_recovered":false,"primary_support":null,"published_description":"Published b-type grouping with GLYR1","reference_doi":"10.1186/1471-2148-12-101","relationship":"NSD second domains plus GLYR1","sensitivity_recovered":false,"sensitivity_support":null,"tested_leaves":["O96028_PWWP2","Q49A26_PWWP1","Q96L73_PWWP2","Q9BZ95_PWWP2"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. An additional comparator nested in a group can prevent exact bipartition matching without disproving broad affinity.","interpretation":"Recovered with both primary support thresholds; compare sensitivity before interpretation.","primary_recovered":true,"primary_support":{"sh_alrt":99.5,"ufboot":100.0},"published_description":"ZMYND/BS69 subgroup","reference_doi":"10.1186/1471-2148-12-101","relationship":"ZMYND subgroup including mouse comparator","sensitivity_recovered":true,"sensitivity_support":{"sh_alrt":98.8,"ufboot":99.0},"tested_leaves":["Q15326_PWWP1","Q8R5C8_PWWP1","Q9ULU4_PWWP1"]},{"comparison_scope":"Exact split in this differently sampled dataset, with the explicitly listed comparators. 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