Meta-Storms 2 is the standalone implementation of the Microbiome Search Engine (MSE; This is the official software repository of Meta-Storms 2.
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Meta-Storms 2

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Meta-Storms 2 is the standalone implementation of the Microbiome Search Engine (MSE; MSE is a search engine designed to efficiently search a database of microbiome samples and identify similar samples based on phylogenetic or functional relatedness. Meta-Storms 2 consists of the following steps: (i) creating a database composed of reference microbiome samples, and (ii) searching for similar samples in the database with given query microbiome sample(s) via phylogenetic similarities. Meta-Storms 2 relies on an advanced indexing algorithm, providing a fast, and constant, search speed in very large databases.

System Requirement and dependency

Hardware Requirements

Meta-Storms 2 only requires a standard computer with sufficient RAM to support the operations defined by a user. For typical users, this would be a computer with about 2 GB of RAM. For optimal performance, we recommend a computer with the following specs:

RAM: 8+ GB
CPU: 4+ cores, 3.3+ GHz/core

Software Requirements

OpenMP library is the C/C++ parallel computing library. Most Linux releases have OpenMP already been installed in the system. In Mac OS X, to install the compiler that supports OpenMP, we recommend using the Homebrew package manager:

brew install gcc --without-multilib

Installation guide

Automatic Installation (recommended)

At present, Meta-Storms 2 provides a fully automatic installer for easy installation.

a. Download the package:

git clone	

b. Install by installer:

cd meta-storms

The package should take less than 1 minute to install on a computer with the specifications recommended above.

The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.

Manual Installation

If the automatic installer fails, Meta-Storms 2 can still be installed manually.

a. Download the package:

git clone	

b. Configure the environment variables (the default environment variable configuration file is “~/.bashrc”):

export MetaStorms=Path to Meta-Storms 2
export PATH=”$PATH:$MetaStorms/bin/”
source ~/.bashrc

c. Compile the source code:

cd meta-storms


The test code and datasets for reproducing the results of manuscript "Model-free disease classification across cohorts via microbiome search" is available here (Linux X86_64 / Mac OS X, ~ 892 MB). See “Readme.txt” in the package for usage and details.