https://github.com/ncbi/tree-tool
Incremental building of phylogenetic distance trees
https://github.com/ncbi/tree-tool
bioinformatics bioinformatics-tool data-analysis distance-measures evolution phylogenetic-trees
Last synced: about 1 month ago
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Incremental building of phylogenetic distance trees
- Host: GitHub
- URL: https://github.com/ncbi/tree-tool
- Owner: ncbi
- License: other
- Created: 2016-01-20T19:00:53.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2026-01-25T20:06:10.000Z (about 2 months ago)
- Last Synced: 2026-01-26T11:07:12.261Z (about 2 months ago)
- Topics: bioinformatics, bioinformatics-tool, data-analysis, distance-measures, evolution, phylogenetic-trees
- Language: HTML
- Homepage:
- Size: 75.9 MB
- Stars: 27
- Watchers: 10
- Forks: 10
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Phylogenetic Distance Tree
Build a least squares distance tree given a matrix of dissimilarities.
Build a large tree incrementally.
Taxonomy miscongruence of a phylogenetic tree
General data analysis tools.
## [Documentation at Wiki](https://github.com/ncbi/tree-tool/wiki)
## Theoretical papers
[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)
[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)
## Application papers
Goldfarb, 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).
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.
Nucleic acids research, gkae1038. Advance online publication. PMID: [39526381](https://doi.org/10.1093/nar/gkae1038)
[Interactive tree of _Eukaryota_](https://html-preview.github.io/?url=https://github.com/ncbi/tree-tool/blob/master/phylogeny/Trees/Eukaryota.html)
Shmakov SA, Barth ZK, Makarova KS, Wolf YI, Brover V, Peters JE, Koonin EV.
Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems.
bioRxiv [Preprint]. 2023 Mar 3:2023.03.03.530964. doi: 10.1101/2023.03.03.530964.
Update in: Nucleic Acids Res. 2023 Jun 07;: PMID: [37090614](https://pubmed.ncbi.nlm.nih.gov/37090614/); PMCID: PMC10120712.
Rogozin IB, Saura A, Bykova A, Brover V, Yurchenko V.
Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes.
Microorganisms. 2023 Jan 16;11(1):229.
doi: 10.3390/microorganisms11010229. PMID: [36677521](https://pubmed.ncbi.nlm.nih.gov/36677521/); PMCID: PMC9862619.
Kennedy AH, Schoch CL, Marrero G, Brover V, Robbertse B.
Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in _Colletotrichum_.
Plant Dis. 2022 Jun;106(6):1573-1596.
doi: 10.1094/PDIS-09-21-2083-SR. Epub 2022 May 10. PMID: [35538602](https://pubmed.ncbi.nlm.nih.gov/35538602/); PMCID: PMC9196201.
[Interactive tree of _Colletotrichum_ (and whole Fungi)](https://ftp.ncbi.nlm.nih.gov/pub/robberts/BLOG/ColletotrichumR19.html)
Novel tool to build large phylogenetic trees with applications to NCBI genomes and rRNA sequences,
November 2021,
[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&linkId=6188627bd7d1af224bc54e3a&showFulltext=true)
Conference: CSHL GENOME INFORMATICS 2021