A suite of methods and models for studying evolutionary radiations

Scripts used for the analysis of phylosymbiosis in coral reef invertebrates

Analysis for cophylogeny in coral reef invertebrates

Pipeline for community ecology and phylogenetic comparative methods of sponge-microbe symbioses

scripts for predicting phylogenetic marker genes

An updated R Markdown thesis template using the bookdown package

rrtools: Tools for Writing Reproducible Research in R

Neural networks for microbe-metabolite interaction analysis

DAS Tool

Analysis code for a manuscript on community similarity computation

R package for calculating specificity in ecological data

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Null modelling of phylogenetic nearest taxon distances for individual taxa

functions for analyzing phyloseq data

These analyses use a three step approach to cluster highly similar amino acid sequences from multiple genomes as 'functional traits', annotates them via KEGG and generates matrices in R for ecologi…

Versatile open-source tool for microbiome analysis

A robust and fast clustering method for amplicon-based studies

SINA - Reference based multiple sequence alignment

Existing tools based ‘assembly pipeline’ and ‘gap pipeline’ for paired-end MiSeq Illumina reads

Biblatex styles for journals of environmental microbiology and microbial ecology

Simple and crude scripts that I've written for my own work that may be of help to others with similar tasks

A metagenomic and isolate assembly and analysis pipeline built with AMOS

⚡ ♒ Rapid prokaryotic genome annotation

Collection of various scripts

SortMeRNA: next-generation sequence filtering and alignment tool

Cutadapt removes adapter sequences from sequencing reads

Code and examples for JHU Computational Genomics class

Toolkit for processing sequences in FASTA/Q formats