Genome

Soluto is a great application that allows you to analyze your boot time, view which applications are slowing it down and improve it as you like. Soluto's goal is to bring an end to the frustrations PC users encounter. We have all come to expect our computers to be sluggish or unresponsive at...

My ID Protector self-discovers anything on your computer that looks potentially like your personal and sensitive information. In addition to simply discovering your personal regulated private information, My ID Protector has fully integrated tools allowing you to: Encrypt Files, Delete Files,...

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,...


Platforms: Windows, Mac, Linux

BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.


Platforms: Windows, Mac, Linux

Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.


Platforms: Windows, Mac, Linux

Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent, Parse::Yapp and Perl-byacc. Some can parse human genome annotations in minutes. Documentation and user guides are provided.


Platforms: Windows, Mac, Linux

GenoViz provides software applications and re-usable components for genomics data visualization and data sharing. One included project is IGB: the Integrated Genome Browser. Documentation is available from http://sourceforge.net/apps/trac/genoviz/


Platforms: Windows, Mac, BSD, Linux

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of...


Platforms: Mac

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr.


Platforms: Windows, Mac, Linux

Oxidizer is a Recursive Fractal Flame editor and renderer for OS X. It is designed to be compatible with the flam3 suite and the Electric Sheep screen saver allowing the user to render flames and sheep movies along with the interactive creation of original flames. Oxidizer is a universal binary....


Platforms: Mac

This program is a parser that abstract a data structure from a given Entrez Gene record, and users of the parser can decide what to do/extract from the data structure. Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent,...


Platforms: Windows, Mac, *nix, Perl, BSD Solaris

QT clustering algorithm as described in:Heyer, L. J., Kruglyak, S., Yooseph, S. (1999). Exploring expression data: Identification and analysis of coexpressed genes. Genome Research 9,...


Platforms: Matlab

Welcome to the SRMA home page. SRMA is a short read micro re-aligner for next-generation high throughput sequencing data. Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed...


Platforms: Mac

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists...


Platforms: Mac

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example...


Platforms: Mac

AutoSOME is a new unsupervised multidimensional clustering method for identifying clusters of diverse shapes and sizes from large numerical datasets without prior knowledge of cluster number (BMC Bioinformatics, 11:117). Given the general nature of data clustering, AutoSOME has utility for a wide...


Platforms: Mac

PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true...


Platforms: Mac

A collection of various perl scripts that utilize bioperl modules for use in bioinformatics analysis. Tools are included for processing microarray data, next generation sequencing data, data file format conversion, querying datasets, and general high level analysis of datasets. This tool box of...


Platforms: Mac

Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals. Features Displays haplotype similarity by color; Sorts accessions automatically to...


Platforms: *nix

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.


Platforms: *nix