{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2023:I6HYMXKK3W6TGC2MBLV7SBL2WT","short_pith_number":"pith:I6HYMXKK","canonical_record":{"source":{"id":"2301.00992","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.PE","submitted_at":"2023-01-03T07:54:01Z","cross_cats_sorted":[],"title_canon_sha256":"3e73433d8b871cb7af9f864769c0c97eb4cfdf6ad0f35ae3c7ab4540a3de6810","abstract_canon_sha256":"92785141ba5005d963e5873b6abf12707b9d0ba20b3ad00369d2862e90019bf3"},"schema_version":"1.0"},"canonical_sha256":"478f865d4addbd330b4c0aebf9057ab4f1b9b0f8b8b017d409c1f5f8cd626290","source":{"kind":"arxiv","id":"2301.00992","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2301.00992","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"arxiv_version","alias_value":"2301.00992v2","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2301.00992","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_12","alias_value":"I6HYMXKK3W6T","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_16","alias_value":"I6HYMXKK3W6TGC2M","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_8","alias_value":"I6HYMXKK","created_at":"2026-07-05T06:00:35Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2023:I6HYMXKK3W6TGC2MBLV7SBL2WT","target":"record","payload":{"canonical_record":{"source":{"id":"2301.00992","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.PE","submitted_at":"2023-01-03T07:54:01Z","cross_cats_sorted":[],"title_canon_sha256":"3e73433d8b871cb7af9f864769c0c97eb4cfdf6ad0f35ae3c7ab4540a3de6810","abstract_canon_sha256":"92785141ba5005d963e5873b6abf12707b9d0ba20b3ad00369d2862e90019bf3"},"schema_version":"1.0"},"canonical_sha256":"478f865d4addbd330b4c0aebf9057ab4f1b9b0f8b8b017d409c1f5f8cd626290","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T06:00:35.809273Z","signature_b64":"/q94BUhxk366EFXRLvfOyutOOryXnI32J//1VLEyUrJ02ZthXnHJQSo1idSDQKd6//fceYnqbFUx1Qi2YBx9AQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"478f865d4addbd330b4c0aebf9057ab4f1b9b0f8b8b017d409c1f5f8cd626290","last_reissued_at":"2026-07-05T06:00:35.808712Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T06:00:35.808712Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2301.00992","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T06:00:35Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"fVCFC/iAIDy5Xu/7GHA6pXQqGyGS5bD6kbIWL3xulzp5qvbpzftIjfysGR/YvrtB6uv9nz6UYklJ2T/xRlbwBw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-07T12:39:20.277882Z"},"content_sha256":"9d2e0e7a84a9f3b62db8cb7790f468c7a0face48af63d518a663df960e99a883","schema_version":"1.0","event_id":"sha256:9d2e0e7a84a9f3b62db8cb7790f468c7a0face48af63d518a663df960e99a883"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2023:I6HYMXKK3W6TGC2MBLV7SBL2WT","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees by Aligning Lineage Taxon Strings","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.PE","authors_text":"Caroline Colijn, Louxin Zhang, Niloufar Abhari, Yufeng Wu","submitted_at":"2023-01-03T07:54:01Z","abstract_excerpt":"The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature and there are excellent tools available for inferring phylogenetic trees from a large number of biomolec"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2301.00992","kind":"arxiv","version":2},"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/2301.00992/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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T06:00:35Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Tgv8lommv8euh2JfydmQBPVoeeGdgaskmSj3LqbG7qNeNAihIdRSWTBn1l3XHvj49AbAYCBWYPnlepEFd4k4BQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-07T12:39:20.278243Z"},"content_sha256":"77c74b23073db756df0f5ae06d16104c572094bbcf8365ef0b7dc4821c1281d8","schema_version":"1.0","event_id":"sha256:77c74b23073db756df0f5ae06d16104c572094bbcf8365ef0b7dc4821c1281d8"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/bundle.json","state_url":"https://pith.science/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/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":"2026-07-07T12:39:20Z","links":{"resolver":"https://pith.science/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT","bundle":"https://pith.science/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/bundle.json","state":"https://pith.science/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/state.json","well_known_bundle":"https://pith.science/.well-known/pith/I6HYMXKK3W6TGC2MBLV7SBL2WT/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2023:I6HYMXKK3W6TGC2MBLV7SBL2WT","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":"92785141ba5005d963e5873b6abf12707b9d0ba20b3ad00369d2862e90019bf3","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.PE","submitted_at":"2023-01-03T07:54:01Z","title_canon_sha256":"3e73433d8b871cb7af9f864769c0c97eb4cfdf6ad0f35ae3c7ab4540a3de6810"},"schema_version":"1.0","source":{"id":"2301.00992","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2301.00992","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"arxiv_version","alias_value":"2301.00992v2","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2301.00992","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_12","alias_value":"I6HYMXKK3W6T","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_16","alias_value":"I6HYMXKK3W6TGC2M","created_at":"2026-07-05T06:00:35Z"},{"alias_kind":"pith_short_8","alias_value":"I6HYMXKK","created_at":"2026-07-05T06:00:35Z"}],"graph_snapshots":[{"event_id":"sha256:77c74b23073db756df0f5ae06d16104c572094bbcf8365ef0b7dc4821c1281d8","target":"graph","created_at":"2026-07-05T06:00:35Z","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"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2301.00992/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature and there are excellent tools available for inferring phylogenetic trees from a large number of biomolec","authors_text":"Caroline Colijn, Louxin Zhang, Niloufar Abhari, Yufeng Wu","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.PE","submitted_at":"2023-01-03T07:54:01Z","title":"A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees by Aligning Lineage Taxon Strings"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2301.00992","kind":"arxiv","version":2},"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":"sha256:9d2e0e7a84a9f3b62db8cb7790f468c7a0face48af63d518a663df960e99a883","target":"record","created_at":"2026-07-05T06:00:35Z","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":"92785141ba5005d963e5873b6abf12707b9d0ba20b3ad00369d2862e90019bf3","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.PE","submitted_at":"2023-01-03T07:54:01Z","title_canon_sha256":"3e73433d8b871cb7af9f864769c0c97eb4cfdf6ad0f35ae3c7ab4540a3de6810"},"schema_version":"1.0","source":{"id":"2301.00992","kind":"arxiv","version":2}},"canonical_sha256":"478f865d4addbd330b4c0aebf9057ab4f1b9b0f8b8b017d409c1f5f8cd626290","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"478f865d4addbd330b4c0aebf9057ab4f1b9b0f8b8b017d409c1f5f8cd626290","first_computed_at":"2026-07-05T06:00:35.808712Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T06:00:35.808712Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"/q94BUhxk366EFXRLvfOyutOOryXnI32J//1VLEyUrJ02ZthXnHJQSo1idSDQKd6//fceYnqbFUx1Qi2YBx9AQ==","signature_status":"signed_v1","signed_at":"2026-07-05T06:00:35.809273Z","signed_message":"canonical_sha256_bytes"},"source_id":"2301.00992","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:9d2e0e7a84a9f3b62db8cb7790f468c7a0face48af63d518a663df960e99a883","sha256:77c74b23073db756df0f5ae06d16104c572094bbcf8365ef0b7dc4821c1281d8"],"state_sha256":"2653a3abe0ea62c19e1a716918ac4186703363c04a5edb54a478d901a12ec8ad"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"U0haybUkW1IE9UzXs02vkpHToS1pQT5OF1s2in6gfIDx2RWtPXqlk7ItZR2JpJmC9TrSA5TAYUeMf6d2j4CjAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-07T12:39:20.280138Z","bundle_sha256":"bd3e19f2465ee339cba55d695af470e82fb2bcbb773ae2d8189e8d56c571fe6c"}}