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Auspice — interactive visualization tool for phylogenomic and genomic epidemiology data from the Nextstrain platform. Renders Nextstrain JSON datasets as interactive phylogenetic trees, geographic tra

1 shared topic • 1 shared operation

FigTree — interactive Java-based phylogenetic tree viewer for displaying, annotating, and exporting phylogenetic trees produced by BEAST, BEAST2, MrBayes, RAxML, IQ-TREE, or any NEXUS/Newick tree file

1 shared topic • 1 shared operation

Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c

1 shared topic • 1 shared operation

Microreact — web-based visualization platform for genomic epidemiology that combines interactive phylogenetic trees, geographic maps, and timelines with metadata tables synchronized through client-sid

1 shared topic • 1 shared operation

scipy.optimize — Unified interface for numerical optimization in Python. Provides local and global minimization (minimize, differential_evolution, dual_annealing), root finding (root, root_scalar), cu

1 shared topic • 1 shared operation