Our software packages are divided into the following categories:
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.
Java framework for reading, writing, analyzing and manipulating sequence and assembly data. Jillion supports most common data file formats...
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.
Middleware for organizing large chunks of data to free the client from having to encode data storage specifics.
A tool for analyzing and annotating eukaryotic genomic sequences.
The automated Prokaryotic Annotation Pipeline was developed to generate on demand ORF prediction and functional annotation for prokaryotic...
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 tool for predicting if an amino acid substitution and small indel affects protein function based on sequence alignment scores.
A tool for predicting if an amino acid substitution affects protein function based on the degree of conservation of amino acid residues.
A Hierarchical Variant Classifier for Annotated Genomes
VIGOR (Viral Genome ORF Reader) is a web application tool to predict protein sequences encoded in small viral genomes. It determines the...
Statistical tools for the analysis of deep sequencing.
Cloe is a contig visualization and finishing editor written in Java.
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.
PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species...
A tool to identify prophage regions within bacterial genomes.
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.