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
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 in Colletotrichum. 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 of Colletotrichum
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 Conference: CSHL GENOME INFORMATICS 2021