phylogenetic analyses informed by deep mutational scanning data

This repository contains scripts, data, and methods of analysis used in Codon Adaptation Index of Species (CAIS) related projects.

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

A bioinformatics pipeline for analysis of SARS-CoV-2 from wastewater samples

Dissimilarity Overlap Curve analysis

A user-friendly workflow for phylogenomics

Statistical Rethinking course at MPI-EVA from Dec 2018 through Feb 2019

Cross-disease comparison of case-control gut microbiome studies

A toolkit for analyzing and visualizing phylogenetic placement data

Massively parallel phylogenetic placement of genetic sequences

Statistical Analysis of Metagenomic Profiles

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA

MicrobeDB v2

annotation pipeline for microbial genomes and metagenomes

Versatile open-source tool for microbiome analysis