Category Archives: Software

A description of the software that the lab develops and publishes

Virtual Machine Images

We have several virtual machine images that we use for courses and other reasons.

You can use most of these with Virtual Box, a free emulator.

  • 2015 SDSU Metagenomics Workshop Image [image no longer available]

Here are instructions for setting up a Virtual Box Virtual Machine.

If the disk is limited for space, you can share a folder with your host machine. Here are instructions for setting up a shared folder on your machine


A List of software developed in our lab

Please use the tools Q&A site ( if you have any question related to the tools listed below.

Jump to:

Tools for metagenomic and metatranscriptomic data
Tools for genomic data
Tools for phage data
Tools for mobile and other handheld devices
Tools for coral reef biology

Tools for metagenomic and metatranscriptomic data

logo_prinseq PRINSEQ
A sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular format that can be used for quality control steps. PRINSEQ is available as both standalone and web-based version.
logo_tagcleaner TagCleaner
Tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based version.
logo_deconseq DeconSeq
Tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based version.
logo_riboPicker riboPicker
Tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too. riboPicker is available as both standalone and web-based version.


A statistical tool written by Beltran Rodriguez in Forest Rohwer’s lab. We used it to analyze the first pyrosequencing-based metagenomes (from the Soudan Mine in Minnesota) and the original Sargasso Samples from Venter. You can download the source code of Xipe-totec, or use the online version of the tool.


Metagenome annotation services across several platforms of technology, which include CGI scripting and web services (RTMg.web), the new Android cell phone operating system (RTMg.mob), and all OpenSocial-based social network sites (RTMg.os)
logo_seed SEED database tools
The SEED database of microbial genomes is used in many projects. We work with our colleagues at Argonne National Laboratory to develop the SEED and tools that access and use it.
crAss: Reference-independent comparative metagenomics using cross-assembly
crAss is a web tool for comparative metagenomics using cross-assembly.
FOCUS: An Alignment-Free Model To Identify Organisms In Metagenomes Using Non-Negative Least Squares UsageFOCUS, an innovative and agile model to profile and report organisms present in metagenomic samples based on composition usage without sequence length dependencies.
 sf_logo SUPER-FOCUS: An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.
ccom CCOM:  This web-based tool is used to reconstruct the uncultured genome from environmental samples.

Tools for genomic data

Software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.

Tools for phage data


We are developing the PHage ANnotation TOols and MEthods (PhAnToME) site in collaboration with researchers in Arizona, Florida, and Virginia. Most of those tools are being released through that website.


PHAge Classification Tool Set or PHACTS is a web based program that is used to calculate whether a phage is lytic or lysogenic.


Phage Proteomic Tree
A phylogentic classic that is so good its in text books!


The Phage SEED
Database for annotating and comparing phage genomes.


The Phage Biobike
A graphical programming language for non-computer scientists to analyze biological data.


Phage Eco-Locator
Tool to identify phages in metagenomes.


A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies.

Tools for mobile and other handheld devices

mobilemetagenomics2 Mobile Metagenomics
An app that allows you to annotate metagenomes using android phones. The source code is hosted on Google Code. Also check out our youtube video!
genomesearch GenomeSearch
An interactive app for searching genomes at the SEED.


Documentation for a tool which handles custom capture, save, and viewing of images taken with an Allied Vision Technologies camera.
Source code is available on github at:

Tools for coral reef biology

Barracuda Coral Reef Photography
New software that allows you to analyze images from coral reefs and identify movement from the background noise.