Streamlit webapp for the annotation of Nextstrain Auspice v2 JSON with lineage labels based on genotype representation.

Munge GenBank files into FASTA and tab-separated metadata

R script for genetic diversity analyses and plotting

Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.

The ARTIC field bioinformatics pipeline

The Zika bioinformatics pipeline

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

Consensus sequences for U.S. H5N1 clade 2.3.4.4b

Regularly used bioinformatics script for different purposes

Phylogenetic orthology inference for comparative genomics

A genome browser designed for complex structural variants and long reads.

Efficient phylogenetic clustering of viral sequences

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)

Code from Lin et al., "The number and pattern of viral genomic reassortments are not necessarily identifiable from segment trees", 2024; msae078.

Sydney Phylogenetics Workshop

A Jekyll version of the "Prologue" theme by HTML5 UP

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Robs manual for the computational genomics and bioinformatics class.

Code used to analyse and plot metadata of metagenomic binning tools

Interactive tutorials for using scikit-bio in biological research

zDB: comparative bacterial genomics made easy

A basic introduction to Biopython, intended for a classroom based workshop

Commonly used phylogenetic methods, Monash HPC access and basic bioinformatics

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

A course in the theory and practice of phylogenetic inference from DNA sequence data

Interactive lessons in bioinformatics.

'ggplot2' Based Publication Ready Plots