Microreact

EpiEstim — CRAN R package from the MRC Centre for Global Infectious Disease Analysis for estimating the time-varying (instantaneous) reproduction number R_t from epidemic incidence time series. Implem

2 shared topics • 1 shared operation

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 • 2 shared operations

Picante routing skill for community phylogenetics, phylogenetic diversity, and comparative analyses in R. Use this skill when users mention picante, phylogenetic diversity, PD, MPD, MNTD, NRI, NTI, se

1 shared topic • 2 shared operations

BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

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