Tools
Software tools developed by CEIRR investigators for researching influenza and related pathogens.
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H5Nx Nextclade datasets
Clade assignment and quality control for H5Nx, H5Nx clade 2.3.4.4, and H5Nx clade 2.3.2.1.
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H5Nx Nextstrain builds
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.
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Imprinting Calculator
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).
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PARNAS
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.
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classLog
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.
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Nextstrain
Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data.
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Nextstrain Groups
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
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polyclonal
polyclonal models mutational escape from polyclonal antibodies using deep mutational scanning data.
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Flu Strain Compare
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.
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PD-stats
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.
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smot
smot is a command-line application for manipulating phylogenies that includes algorithms for subsampling, filtering and classifying phylogenetic trees.