Software

Manipulation of input and output files related to whole-genome shotgun assembly. Currently maintained at CBCB at the University of Maryland.

CABOG assembles long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.

This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid.

High throughput assembly of amplicon reads for virus-sized genomes.

High throughput PCR primer design software.

A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses.

Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003.

A microbial gene-finding system, especially in bacteria, archaea, and viruses. Currently maintained at CBCB at the University of Maryland.

A tool for analyzing and annotating eukaryotic genomic sequences.

Web-based gene evaluation and genome annotation tool to view, modify, and store annotation for prokaryotic and eukaryotic genomes.

A eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene...

A Hierarchical Variant Classifier for Annotated Genomes

Statistical tools for the analysis of deep sequencing.

The DAGchainer software computes chains of syntenic genes found within complete genome sequences.

DNA sequence analysis tools including ESTmapper, Snapper (for mapping reads), and ATAC (for aligning genomes).

MUMmer is a system for rapidly aligning entire genomes (draft or complete). Currently maintained at CBCB at the University of Maryland.

A NIAID Bioinformatics Resource Center (BRC) containing in depth curatorial analysis of six target organisms from the list of NIAID...

A tool to identify prophage regions within bacterial genomes.

Sybil is a web-based software package for comparative genomics.

An open source suite of tools for high-performance comparative metagenomics.

Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis and normalization package.

Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays.

Scripts to identify and filter out false positive SNP calls that are present in raw data from Affymetrix GeneChip® resequencing arrays.

TM4 is a suite of open source software tools that manage and analyze data from microarray experiments.

The APEX tool is an implementation of the Absolute Protein Expression quantitation technique, computing protein abundance values for...

Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.