LAVA: Longitudinal Analysis of Viral Alleles

High accuracy single molecule Nanopore reads using the MrHAMER pipeline

Code for the analysis and data visualization found in the paper entitled "Genomic epidemiology of dengue virus 2 and 3 reveals repeated introductions and exportations of several lineages in Colombia."

This repository includes the model code + GUI for the research paper "Endogenous viral mutations, evolutionary selection, and containment policy design" published in the Journal of Economic Interaction and Coordination. You can find the paper here: https://link.springer.com/article/10.1007/s11403-021-00344-3

R package for entropy-informed detection of emerging viral variants and genomic surveillance. Implements per-site Shannon entropy, Gaussian mixture model site selection, Hellinger distance, and non-parametric change-point detection. Validated on SARS-CoV-2 Spike protein sequences from NCBI and GISAID databases.

Automated maximum-likelihood phylogeny pipeline for viral families. Discovers species via NCBI Taxonomy, downloads from GenBank, aligns with MAFFT, builds trees with FastTree (broad) and IQ-TREE (refined), and annotates internal nodes by LCA. Supports multi-marker concatenation for large DNA virus families.