Install QIIME 1

update 2018: consider using the new version → QIIME 2

Install QIIME-1.9.1 using conda (Ubuntu / Linux)

1) Install Miniconda


bash # run installation

2) Install QIIME

conda create -n qiime1 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda

conda install psutil

→ PackagesNotFoundError (2019)

# test QIIME installation

conda activate qiime1 -t

→ Edit .qiime_config

# Start QIIME

conda activate qiime1

# Finish QIIME

conda deactivate

Install GNU R and additional packages required for QIIME

→ DESeq2 (required in

→ CSS (required in

# install fastq-join (ea-utils) required for qiime

sudo apt-get install ea-utils # Ubuntu/Linux (or, compile using make)

→ install usearch

Install QIIME in Virtual Machine (Windows)

# download and decompress latest version of → QIIME Virtual Box image


# activate virtual machine