Genome

SnipPeep is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser. Platforms: Mac

Timina is a Java web-based application for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences. Platforms: Mac, BSD, Linux

WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study. Platforms: Windows, Mac, Linux

dbSNPtool starts a GUI to return polymorphism data from dbSNPwww.ncbi.nih.gov/SNP Calling dbsnptool start the GUI, SNP % records are returned based on keyword. Each result is presented in a % listbox, clicking on the entry loads the sequence into the sequence %viewer. Information is presenting... Platforms: Matlab

MCGH is a Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome. M-CGH allows us to visualize the copy number changes... Platforms: Matlab

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description... Platforms: Matlab

The script is a Matlab implementation of reference gene selection reported inJo Vandesompele et al, "Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes", Genome Biology 2002, 3 (7). Platforms: Matlab

Returns the contingency tables for several markers in case control study.Simple count of SNP count according to the type of polymorphism. Platforms: Matlab

GenericLevenshtein Yet another Implementation of Levenshtein Distance GenericLevenshtein is an implementation of Minimum Edit Distance, also called Levenshtein Distance, written by Ramon Ziai and Niels Ott. This algorithm is very popular and it is often used to compute the similarity of... Platforms: Mac

Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Platforms: Mac

Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate... Platforms: Mac

The BLAST Ring Image Generator (BRIG) is a cross-platform JAVA application, it has a graphical user interface, which takes the user step-by-step through the configuration of a genome circular visualization. Platforms: Mac

UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install. Features: * Multiple sequence alignment using MUSCLE 3, KAlign, Clustal; * HMM profiles build and search, based on the source of HMMER 2 and HMMER... Platforms: Mac

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the... Platforms: Mac

Open up the power of 3D environments to researchers working with genomic information. Visualizing large amount of information at disparate locations in the genome while using a vast variety of algoritms makes Sockeye the number one tool for scientists working on genomic data. Platforms: Mac

bedtools: a flexible suite of utilities for comparing genomic features. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.... Platforms: Mac

JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy).... Platforms: Mac

BaseByBase is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly... Platforms: Mac

The Annotate Sequence with GFF File makes it very easy to annotate a sequence with annotations from a GFF file (Generic Feature Format). A GFF file does not contain any sequence information, it only contains a list of annotations. You can read more about the format at... Platforms: Mac

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies This tool aims to identifying structural variations with both clustering and... Platforms: *nix