PoonLab

covizu

Rapid analysis and visualization of coronavirus genome variation

OpenRDP

An open-source re-implementation of the RDP4 recombination detection program

sam2conseq

sierra-local

Retrieve HIVdb algorithm as XML and apply locally to HIV sequences

bayroot

Bayesian root-to-tip regression for dating reservoir sequences

HexSE

Simulation of molecular evolution with overlapping reading frames

Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference

MiCall-Lite

Pipeline for processing FASTQ data from an Illumina MiSeq for human RNA virus (HIV, hepatitis C virus) genotyping

gromstole

Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples

twt

Generic framework for the coalescent simulation of pathogen trees within host trees in R

courses

ovrf-viz

Review article on overlapping reading frames in viruses

plodex

Interactive visualization of SARS-CoV-2 variants

clmp

Genetic clustering with Markov-modulated Poisson processes

cophylo

Data and scripts associated with manuscript on Tree Metrics of Cophylogeny

fluclades

Genetic taxonomy of influenza A virus subtypes

highlineR

An implementation of LANL's Highlighter web app in R for batch processing and scaling

vindels

Developing an empirical model of sequence insertion and deletion in virus genomes

clustuneR

Implementing clustering algorithms on genetic data and finding optimal parameters through the performance of predictive growth models.

indelrates

Data and scripts used for HIV-1 group M indel rate estimation project

Bioplus

In-house scripts that extend the functionality of Biopython

colgem

Read-only mirror of "colgem" from r-forge SVN.

comet-prot

Book chapter for upcoming Springer book Computational Methods in Protein Evolution

constellations

KaphiShiny

A Shiny web interface for running Kaphi

Poplars

Open-source implementations of popular tools from Los Alamos National Laboratory HIV Database

sup

Sequencing Uncertainty Propagation

test

tn

Optimization of genetic clustering methods by predictive modeling

tuning-disorder-virus

Ensemble classifier of intrinsic protein disorder for viruses