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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.

Building Large Phylogenetic Trees in Log-Linear Time

Epistemic Principle of a Congruence Maximization of a Phylogenetic Tree to External Classifications

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

Interactive tree ofEukaryota

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; 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; 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 inColletotrichum.Plant Dis. 2022 Jun;106(6):1573-1596.doi: 10.1094/PDIS-09-21-2083-SR. Epub 2022 May 10. PMID:35538602; PMCID: PMC9196201.

Interactive tree ofColletotrichum (and whole Fungi)

Novel tool to build large phylogenetic trees with applications to NCBI genomes and rRNA sequences,November 2021,DOI: 10.13140/RG.2.2.16339.71204Conference: CSHL GENOME INFORMATICS 2021