{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2016:SQ3B6TTLTEOKSVPGUZE2DGC5OB","short_pith_number":"pith:SQ3B6TTL","canonical_record":{"source":{"id":"1606.08893","kind":"arxiv","version":3},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2016-06-28T21:23:04Z","cross_cats_sorted":[],"title_canon_sha256":"89ff65d7d693ac1fa8b0bdb2523f0c421315dd483bb73ec37a894598528342c8","abstract_canon_sha256":"7702f4ff114936bdd483a7c0e28f3e40fc2473217d269cd0d9d337e40f642790"},"schema_version":"1.0"},"canonical_sha256":"94361f4e6b991ca955e6a649a1985d7047d42f98af7673d910b1c8b57477856a","source":{"kind":"arxiv","id":"1606.08893","version":3},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1606.08893","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"arxiv_version","alias_value":"1606.08893v3","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1606.08893","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"pith_short_12","alias_value":"SQ3B6TTLTEOK","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_16","alias_value":"SQ3B6TTLTEOKSVPG","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_8","alias_value":"SQ3B6TTL","created_at":"2026-05-18T12:30:44Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2016:SQ3B6TTLTEOKSVPGUZE2DGC5OB","target":"record","payload":{"canonical_record":{"source":{"id":"1606.08893","kind":"arxiv","version":3},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2016-06-28T21:23:04Z","cross_cats_sorted":[],"title_canon_sha256":"89ff65d7d693ac1fa8b0bdb2523f0c421315dd483bb73ec37a894598528342c8","abstract_canon_sha256":"7702f4ff114936bdd483a7c0e28f3e40fc2473217d269cd0d9d337e40f642790"},"schema_version":"1.0"},"canonical_sha256":"94361f4e6b991ca955e6a649a1985d7047d42f98af7673d910b1c8b57477856a","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:45:30.508146Z","signature_b64":"Yj2z18lBLrqYfBKZbnz+6jKeZfesJRMnpd5MHbJKIS7WYt5y+XjUctmVQqqoDW7yXIn32VcnYtsPGn5TpiodAw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"94361f4e6b991ca955e6a649a1985d7047d42f98af7673d910b1c8b57477856a","last_reissued_at":"2026-05-18T00:45:30.507624Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:45:30.507624Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1606.08893","source_version":3,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:45:30Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"q5LzVWfhCVynsgIyuuedTmDrFpuyQ7vcwg6eEzmSmhuELBi8bUY8TRrf6JwBpTUntWyrKpCyP3CgmE27VeZfCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T14:56:45.442069Z"},"content_sha256":"fc741a1cc265154cd5099c92570248a58c76062cf61e71db01fb4005b757e3ed","schema_version":"1.0","event_id":"sha256:fc741a1cc265154cd5099c92570248a58c76062cf61e71db01fb4005b757e3ed"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2016:SQ3B6TTLTEOKSVPGUZE2DGC5OB","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"cs.DS","authors_text":"Chris Whidden, Frederick A. Matsen IV","submitted_at":"2016-06-28T21:23:04Z","abstract_excerpt":"We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better understand the behaviour of phylogenetic methods and recommend parameter choices and diagnostic criteria. The limiting factor in these analyses has been the difficulty in constructing such graphs for large numbers of trees. We also develop the first efficient algorithms for constructing the nearest-neighbor interchange (NNI) and tree bisection-and-reconnection"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1606.08893","kind":"arxiv","version":3},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:45:30Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"WIJXbMgkq2XUE3j960A8IHdx27QzEqtgVCz9TQ6Hi+T32UOf6WRPsZ0oIUFHxpO4mwNy+DcbwfzgG0aIkDL2Dw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T14:56:45.442448Z"},"content_sha256":"ac465739b2bc8fc9003be8dbf26b45c12d39ca6c033fe2192248ea13dae32a0c","schema_version":"1.0","event_id":"sha256:ac465739b2bc8fc9003be8dbf26b45c12d39ca6c033fe2192248ea13dae32a0c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/bundle.json","state_url":"https://pith.science/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-05-28T14:56:45Z","links":{"resolver":"https://pith.science/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB","bundle":"https://pith.science/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/bundle.json","state":"https://pith.science/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/state.json","well_known_bundle":"https://pith.science/.well-known/pith/SQ3B6TTLTEOKSVPGUZE2DGC5OB/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2016:SQ3B6TTLTEOKSVPGUZE2DGC5OB","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"7702f4ff114936bdd483a7c0e28f3e40fc2473217d269cd0d9d337e40f642790","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2016-06-28T21:23:04Z","title_canon_sha256":"89ff65d7d693ac1fa8b0bdb2523f0c421315dd483bb73ec37a894598528342c8"},"schema_version":"1.0","source":{"id":"1606.08893","kind":"arxiv","version":3}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1606.08893","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"arxiv_version","alias_value":"1606.08893v3","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1606.08893","created_at":"2026-05-18T00:45:30Z"},{"alias_kind":"pith_short_12","alias_value":"SQ3B6TTLTEOK","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_16","alias_value":"SQ3B6TTLTEOKSVPG","created_at":"2026-05-18T12:30:44Z"},{"alias_kind":"pith_short_8","alias_value":"SQ3B6TTL","created_at":"2026-05-18T12:30:44Z"}],"graph_snapshots":[{"event_id":"sha256:ac465739b2bc8fc9003be8dbf26b45c12d39ca6c033fe2192248ea13dae32a0c","target":"graph","created_at":"2026-05-18T00:45:30Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"paper":{"abstract_excerpt":"We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better understand the behaviour of phylogenetic methods and recommend parameter choices and diagnostic criteria. The limiting factor in these analyses has been the difficulty in constructing such graphs for large numbers of trees. We also develop the first efficient algorithms for constructing the nearest-neighbor interchange (NNI) and tree bisection-and-reconnection","authors_text":"Chris Whidden, Frederick A. Matsen IV","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2016-06-28T21:23:04Z","title":"Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1606.08893","kind":"arxiv","version":3},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:fc741a1cc265154cd5099c92570248a58c76062cf61e71db01fb4005b757e3ed","target":"record","created_at":"2026-05-18T00:45:30Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"7702f4ff114936bdd483a7c0e28f3e40fc2473217d269cd0d9d337e40f642790","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2016-06-28T21:23:04Z","title_canon_sha256":"89ff65d7d693ac1fa8b0bdb2523f0c421315dd483bb73ec37a894598528342c8"},"schema_version":"1.0","source":{"id":"1606.08893","kind":"arxiv","version":3}},"canonical_sha256":"94361f4e6b991ca955e6a649a1985d7047d42f98af7673d910b1c8b57477856a","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"94361f4e6b991ca955e6a649a1985d7047d42f98af7673d910b1c8b57477856a","first_computed_at":"2026-05-18T00:45:30.507624Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:45:30.507624Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Yj2z18lBLrqYfBKZbnz+6jKeZfesJRMnpd5MHbJKIS7WYt5y+XjUctmVQqqoDW7yXIn32VcnYtsPGn5TpiodAw==","signature_status":"signed_v1","signed_at":"2026-05-18T00:45:30.508146Z","signed_message":"canonical_sha256_bytes"},"source_id":"1606.08893","source_kind":"arxiv","source_version":3}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:fc741a1cc265154cd5099c92570248a58c76062cf61e71db01fb4005b757e3ed","sha256:ac465739b2bc8fc9003be8dbf26b45c12d39ca6c033fe2192248ea13dae32a0c"],"state_sha256":"4955e3200eedc1a90ac1c53b76c98a0331324731ef0e1bf4714627189b88563b"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"RaijUCujBngXS88viySc30yLDWNPNJ0SIMB6A8f9HCyJSit/bo5RCM6IrIqfBlN4s+7+/XCVzurwlQsE/p7cBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T14:56:45.444574Z","bundle_sha256":"71c55e2bbd3872d9815d318da955f3c1f45d428271a8e9ad46dea22d851941fe"}}