Tools for computing and integrating Local Branching Index (LBI) values with Auspice phylogenetic trees

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to rep…

An R package and Bayesian generative model to estimate epidemiological parameters from wastewater concentration measurements over time.

Ultra Brief Intro to Docker and Apptainer

R pkg for Hierarchical Dirichlet Process

Tree inference from mitochondrial mutations

A method for embedding and clustering of tumor mutation trees.

Structured knowledge base of HIV-1/HIV-2.

Tools and protocols for nanopore sequencing of poliovirus in real-time.

Dynamics analysis of Alternative PolyAdenylation from long-reads RNA-seq

Personalised mutual hazard networks: fixed effects in cancer progression modeling

VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data

LaTeX template for a PhD thesis at ETH Zurich

Front-end code for Serratus project website

R package to compute quasispecies diversity (currently under development).

aftermerge: A script for merging paired reads after mapping, based on the locations on the reference genome

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

EasyCodeML: A visual tool for analysis of selection using CodeML

A Python package for probabilistic state space modeling with JAX

Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates

Add biological annotations to variants in a given VCF file.

Single-cell Iso Prep

A viral haplotype reconstruction tool for long reads.

This is an updated mirror of the original PacBio Read Simulator