Reassortment inference

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle

Visualization of effects of mutations to H5 hemagglutinin (HA)

Platform for structure-based visualizations of deep mutation scanning data

High path avian influena outbreak dynamics in North America: 2021-present

Estimates of the fitness effects of mutations to all SARS-CoV-2 proteins

An interactive platform to visualize large amounts of deep mutational scanning data on antibody escape

Clade assignment and quality control for H5Nx, H5Nx clade 2.3.4.4, and H5Nx clade 2.3.2.1.

Avian influenza sequences in builds are annotated and colored by whether sequences were sampled from domestic or wild birds, the avian order of the host species (e.g., Anseriformes, Galliformes, etc…), and North American flyway.

imprinting is an R package to reconstruct birth year-specific probabilities of imprinting to each subtype of influenza A, H1N1, H2N2, H3N2. Reconstructions are done following the methods of (Gostic et al. 2016).

PARNAS identifies taxa that best represent diversity on a phylogenetic tree and can be used to 1) Select most representative taxa, 2) Downsample a large phylogeny while optimally preserving the underlying diversity, 3) Reduce redundancy among genetic/genomic sequences, 4) Identify key diversity groups on a phylogeny.

Implementation of logistic regression for classification of sequences based on a reference set. Classlog is designed to train logistic regression classifiers based on genetic information. Trained classifiers can then be used to assign classification future clades with linear time complexity.

Nextstrain Groups is a feature that allows research labs, public health entities, and other organizations to share their Nextstrain datasets and narratives directly on nextstrain.org

Nextstrain workflow for seasonal influenza analysis

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.

polyclonal models mutational escape from polyclonal antibodies using deep mutational scanning data.

Flu Strain Compare generates visualizations of mutations between pairs of HA sequences. Given two sequences as input, it will output a figure or animation highlighting amino acid and PNGS changes on a representative HA crystal structure. H1pdm and H3 strains are supported.

PD-stats quantifies phylogenetic diversity and associated descriptive statistics for all clades in a phylogeny. The tool can be used to identify clades of viruses that have high relative genetic diversity, or groups of viruses that are more diverse than expected by chance.

smot is a command-line application for manipulating phylogenies that includes algorithms for subsampling, filtering and classifying phylogenetic trees.