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adaptml

Automatically partition a phylogeny according to genetic and ecological data

alphafold

Open source code for AlphaFold.

alphafold_non_docker

AlphaFold2 non-docker setup

alphafold_sm

snakemake wrapper for alphafold

ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2

anvio

An analysis and visualization platform for 'omics data

bigslice

A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data

bioconda-recipes

Conda recipes for the bioconda channel.

buckley_lab_sip_project_protocols

Buckley lab protocols for conducting SIP studies

callm

camisim

CAMISIM: Simulating metagenomes and microbial communities

cldb

Create a local pan-genome CRISPR database

conda_r_skeleton_helper

Cleaning up Conda r-packages

consentrait

Phylogenetic conservatism of functional traits in microorganisms

datasci-boilerplate

Boiler plate code for data science projects

deltagc

GC content simulations for DNA-SIP experimental design

dotfiles

dotfile store

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

enasearch

A Python library for interacting with ENA's API

endor

R-package to simplify tree ensemble models to decision ensemble, calculate feature and interaction importance, and construct variable networks.

find_differential_primers

Code for design of diagnostic PCR primers, and metabarcoding markers.

forager

Finding Orthologous Reads and Genes

gt-pro

gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format

gtl_read_filter_pipeline

Illumina read filtering pipeline for the GTL project

gutsmash

gutSMASH

htssip

An R package for analyzing high throughput sequence stable isotope probing data

humann

HUMAnN 2.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

instrain

Bioinformatics program inStrain

kraken2

The second version of the Kraken taxonomic sequence classification system