{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2026:SUUYKZDR7O7GRYEVS3P4T7KXFL","short_pith_number":"pith:SUUYKZDR","schema_version":"1.0","canonical_sha256":"9529856471fbbe68e09596dfc9fd572ac6232bee7d72af95f739f24c25e8e761","source":{"kind":"arxiv","id":"2606.27942","version":1},"attestation_state":"computed","paper":{"title":"Towards coevolution-aware ancestral sequence reconstruction","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["physics.bio-ph","q-bio.PE"],"primary_cat":"q-bio.BM","authors_text":"Alya Zeinaty, Francesco Zamponi, Leonardo di Bari, Martin Weigt, Pierre Barrat-Charlaix, Saverio Rossi","submitted_at":"2026-06-26T10:32:11Z","abstract_excerpt":"Ancestral sequence reconstruction (ASR) is a powerful approach for studying molecular evolution and the emergence of protein function. Yet most ASR methods assume that sites evolve independently, neglecting the epistatic constraints that shape protein structure, stability, and function. This simplification affects both ancestral inference and its evaluation: maximum-a-posteriori reconstructions may over-concentrate probability into a single over-idealized sequence, whereas independent posterior sampling can generate implausible or poorly functional ancestors. Here, we introduce a coevolution-a"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"2606.27942","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2026-06-26T10:32:11Z","cross_cats_sorted":["physics.bio-ph","q-bio.PE"],"title_canon_sha256":"671ce806710600183a4e4f3d59f7679a146c2e5d766f918e69623205b9d88d38","abstract_canon_sha256":"b485843757a2627f1859c827d28c0980928858e85a730c82ce8e12093aad474c"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-29T01:14:53.357051Z","signature_b64":"/YxRgglUZ0+20UoGWWgSR6+hOyNVGl5xwN1H53qNnr+GzVSNmfEIrwbNZ72adYiWoY8uyjUvlsHyKdPtXZ2QAg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"9529856471fbbe68e09596dfc9fd572ac6232bee7d72af95f739f24c25e8e761","last_reissued_at":"2026-06-29T01:14:53.356592Z","signature_status":"signed_v1","first_computed_at":"2026-06-29T01:14:53.356592Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Towards coevolution-aware ancestral sequence reconstruction","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["physics.bio-ph","q-bio.PE"],"primary_cat":"q-bio.BM","authors_text":"Alya Zeinaty, Francesco Zamponi, Leonardo di Bari, Martin Weigt, Pierre Barrat-Charlaix, Saverio Rossi","submitted_at":"2026-06-26T10:32:11Z","abstract_excerpt":"Ancestral sequence reconstruction (ASR) is a powerful approach for studying molecular evolution and the emergence of protein function. Yet most ASR methods assume that sites evolve independently, neglecting the epistatic constraints that shape protein structure, stability, and function. This simplification affects both ancestral inference and its evaluation: maximum-a-posteriori reconstructions may over-concentrate probability into a single over-idealized sequence, whereas independent posterior sampling can generate implausible or poorly functional ancestors. Here, we introduce a coevolution-a"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.27942","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.27942/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"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"},"aliases":[{"alias_kind":"arxiv","alias_value":"2606.27942","created_at":"2026-06-29T01:14:53.356651+00:00"},{"alias_kind":"arxiv_version","alias_value":"2606.27942v1","created_at":"2026-06-29T01:14:53.356651+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2606.27942","created_at":"2026-06-29T01:14:53.356651+00:00"},{"alias_kind":"pith_short_12","alias_value":"SUUYKZDR7O7G","created_at":"2026-06-29T01:14:53.356651+00:00"},{"alias_kind":"pith_short_16","alias_value":"SUUYKZDR7O7GRYEV","created_at":"2026-06-29T01:14:53.356651+00:00"},{"alias_kind":"pith_short_8","alias_value":"SUUYKZDR","created_at":"2026-06-29T01:14:53.356651+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL","json":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL.json","graph_json":"https://pith.science/api/pith-number/SUUYKZDR7O7GRYEVS3P4T7KXFL/graph.json","events_json":"https://pith.science/api/pith-number/SUUYKZDR7O7GRYEVS3P4T7KXFL/events.json","paper":"https://pith.science/paper/SUUYKZDR"},"agent_actions":{"view_html":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL","download_json":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL.json","view_paper":"https://pith.science/paper/SUUYKZDR","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2606.27942&json=true","fetch_graph":"https://pith.science/api/pith-number/SUUYKZDR7O7GRYEVS3P4T7KXFL/graph.json","fetch_events":"https://pith.science/api/pith-number/SUUYKZDR7O7GRYEVS3P4T7KXFL/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL/action/timestamp_anchor","attest_storage":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL/action/storage_attestation","attest_author":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL/action/author_attestation","sign_citation":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL/action/citation_signature","submit_replication":"https://pith.science/pith/SUUYKZDR7O7GRYEVS3P4T7KXFL/action/replication_record"}},"created_at":"2026-06-29T01:14:53.356651+00:00","updated_at":"2026-06-29T01:14:53.356651+00:00"}