{"id":28512480,"url":"https://github.com/ncbi/tree-tool","last_synced_at":"2026-01-31T17:03:43.330Z","repository":{"id":54841438,"uuid":"50052879","full_name":"ncbi/tree-tool","owner":"ncbi","description":"Incremental building of phylogenetic distance trees","archived":false,"fork":false,"pushed_at":"2026-01-25T20:06:10.000Z","size":79569,"stargazers_count":27,"open_issues_count":0,"forks_count":10,"subscribers_count":10,"default_branch":"master","last_synced_at":"2026-01-26T11:07:12.261Z","etag":null,"topics":["bioinformatics","bioinformatics-tool","data-analysis","distance-measures","evolution","phylogenetic-trees"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ncbi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2016-01-20T19:00:53.000Z","updated_at":"2026-01-25T20:06:13.000Z","dependencies_parsed_at":"2025-10-17T12:21:43.306Z","dependency_job_id":"6074dd8b-3065-4fd3-bccc-f1b6cfc760f6","html_url":"https://github.com/ncbi/tree-tool","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ncbi/tree-tool","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2Ftree-tool","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2Ftree-tool/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2Ftree-tool/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2Ftree-tool/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ncbi","download_url":"https://codeload.github.com/ncbi/tree-tool/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2Ftree-tool/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28948356,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-31T14:26:55.697Z","status":"ssl_error","status_checked_at":"2026-01-31T14:26:52.545Z","response_time":128,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bioinformatics-tool","data-analysis","distance-measures","evolution","phylogenetic-trees"],"created_at":"2025-06-09T00:38:08.242Z","updated_at":"2026-01-31T17:03:43.325Z","avatar_url":"https://github.com/ncbi.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Phylogenetic Distance Tree\n\nBuild a least squares distance tree given a matrix of dissimilarities.\n\nBuild a large tree incrementally.\n\nTaxonomy miscongruence of a phylogenetic tree\n\nGeneral data analysis tools.\n\n## [Documentation at Wiki](https://github.com/ncbi/tree-tool/wiki)\n\n\n## Theoretical papers\n\n[Building Large Phylogenetic Trees in Log-Linear Time](https://github.com/ncbi/tree-tool/blob/master/phylogeny/doc/inc_ls_dist_tree/inc_ls_dist_tree.pdf)\n\n[Epistemic Principle of a Congruence Maximization of a Phylogenetic Tree to External Classifications](https://github.com/ncbi/tree-tool/blob/master/phylogeny/doc/tax_miscongruence/tax_miscongruence.pdf)\n\n## Application papers\nGoldfarb, T., Kodali, V. K., Pujar, S., Brover, V., Robbertse, B., Farrell, C. M., Oh, D. H., Astashyn, A., Ermolaeva, O., Haddad, D., Hlavina, W., Hoffman, J., Jackson, J. D., Joardar, V. S., Kristensen, D., Masterson, P., McGarvey, K. M., McVeigh, R., Mozes, E., Murphy, M. R., … Murphy, T. D. (2024). \nNCBI RefSeq: reference sequence standards through 25 years of curation and annotation. \nNucleic acids research, gkae1038. Advance online publication. PMID: [39526381](https://doi.org/10.1093/nar/gkae1038)\n\n[Interactive tree of _Eukaryota_](https://html-preview.github.io/?url=https://github.com/ncbi/tree-tool/blob/master/phylogeny/Trees/Eukaryota.html)\n\nShmakov SA, Barth ZK, Makarova KS, Wolf YI, Brover V, Peters JE, Koonin EV. \nWidespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems. \nbioRxiv [Preprint]. 2023 Mar 3:2023.03.03.530964. doi: 10.1101/2023.03.03.530964. \nUpdate in: Nucleic Acids Res. 2023 Jun 07;: PMID: [37090614](https://pubmed.ncbi.nlm.nih.gov/37090614/); PMCID: PMC10120712.\n\nRogozin IB, Saura A, Bykova A, Brover V, Yurchenko V. \nDeletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes. \nMicroorganisms. 2023 Jan 16;11(1):229. \ndoi: 10.3390/microorganisms11010229. PMID: [36677521](https://pubmed.ncbi.nlm.nih.gov/36677521/); PMCID: PMC9862619.\n\nKennedy AH, Schoch CL, Marrero G, Brover V, Robbertse B. \nPublicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in _Colletotrichum_. \nPlant Dis. 2022 Jun;106(6):1573-1596. \ndoi: 10.1094/PDIS-09-21-2083-SR. Epub 2022 May 10. PMID: [35538602](https://pubmed.ncbi.nlm.nih.gov/35538602/); PMCID: PMC9196201.\n\n[Interactive tree of _Colletotrichum_ (and whole Fungi)](https://ftp.ncbi.nlm.nih.gov/pub/robberts/BLOG/ColletotrichumR19.html)\n\nNovel tool to build large phylogenetic trees with applications to NCBI genomes and rRNA sequences,\nNovember 2021,\n[DOI: 10.13140/RG.2.2.16339.71204](https://www.researchgate.net/publication/355982339_Novel_tool_to_build_large_phylogenetic_trees_with_applications_to_NCBI_genomes_and_rRNA_sequences?channel=doi\u0026linkId=6188627bd7d1af224bc54e3a\u0026showFulltext=true)\nConference: CSHL GENOME INFORMATICS 2021\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fncbi%2Ftree-tool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fncbi%2Ftree-tool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fncbi%2Ftree-tool/lists"}