JCVI: Research / Software
 
 
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Sequencing/Assembly

AMOS

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

CABOG

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

DNA Barcode Deconvolution

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

Elvira

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

JCVI Primer Designer

High throughput PCR primer design software.

Lucy

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

TIGR Assembler

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

TIGR SSS

Middleware for organizing large chunks of data to free the client from having to encode data storage specifics.

Gene Finding

Glimmer

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

Annotation

AAT

A tool for analyzing and annotating eukaryotic genomic sequences.

Manatee

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

PASA

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

PROVEAN

A tool for predicting if an amino acid substitution and small indel affects protein function based on sequence alignment scores.

SIFT

A tool for predicting if an amino acid substitution affects protein function based on the degree of conservation of amino acid residues.

VariantClassifier

A Hierarchical Variant Classifier for Annotated Genomes

Genome Analysis

ANDES Tools

Statistical tools for the analysis of deep sequencing.

DAGchainer

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

k-mer Tools

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

MUMmer

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

Pathema

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

PhageFinder

A tool to identify prophage regions within bacterial genomes.

Sybil

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

Metagenomics Analysis

Metarep

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

Microarray Tools

Ginkgo

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

Magnolia

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

SNP Filter Scripts

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

TM4

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

Proteomics Tools

APEX

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

Cloud

JCVI Cloud BioLinux

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