Software
ARG-Net
A deep neutral network to detect the antibiotics resistance genes and predict their resistance classes based on the sequence data.
Tool type: Python and web application
Publication: Coming soon
EiGEN
A web application to interactively explore the complete global phylogenetic diversity of SARS-CoV-2 genomes. It allows instant analysis of the user-uploaded sequences to determine their phylogenetic positions and mutations on the global context.
Tool type: Web application
Publication: Coming soon
GGtree
An R package for flexible annotation, visualization and analysis of phylogenetic related data.
Tool type: R
Publication: Yu G, Smith D, Zhu H, Guan Y, Lam TT (2017). “ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.” Methods in Ecology and Evolution, 8, 28-36.
GWTCLR
A geographically weighted temporally correlated logistic regression model to estimate the correlations between variables (e.g. disease incidence and climate data) in spatiotemporal space.
Tool type: Mathematica
Publication: Liu, Y., Lam, KF., Wu, J.T., Lam, T.T. Geographically weighted temporally correlated logistic regression model. Sci Rep 8, 1417 (2018).
TIPars
A fast and robust method to update the existing phylogenetic tree with new sequences utilizing the ancestral sequences and parsimony criterion.
Tool type: Java and Web application
Publication: Ye Y, Shum M, Tsui J, Yu G, Smith D, Zhu H, Wu J, Guan Y, Lam TT. Robust expansion of phylogeny for fast-growing genome sequence data. (2022) bioRxiv 2021.12.30.474610;