Software: Genome

 
Integrated Genome Browser 6.6.3 B 10023Integrated Genome Browser Team

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself. IGB is implemented using the Java programming language ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 8.4 MBReleased: 12 March, 2012
Download: http://sourceforge.net/projects/genoviz/files/IGB%206.5/igb.zip/download
Savant Genome Browser for Linux 1. 3. 2001Computational Biology Lab

Savant Genome Browser is a handy, easy to use, Java based visualization application specially designed for genomic data. It was primarily developed for visualizing high throughput (aka next generation) sequencing data, although it can be used to visualize virtually any genome-based sequence, point, interval, or continuous dataset.

FEATURES:

Savant Genome Browser for Linux 1. 3. 2001 by Computational Biology Lab
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 17.4 MBReleased: 25 March, 2012
Download: http://compbio.cs.toronto.edu/savant/dist/v1_3_1/lin/Savant-1.3.1-Linux-x86-Install
Savant Genome Browser for Mac OS X 1. 3. 2001Computational Biology Lab

Savant Genome Browser is a handy, easy to use, Java based visualization application specially designed for genomic data. It was primarily developed for visualizing high throughput (aka next generation) sequencing data, although it can be used to visualize virtually any genome-based sequence, point, interval, or continuous dataset.

FEATURES:

Savant Genome Browser for Mac OS X 1. 3. 2001 by Computational Biology Lab
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 17.4 MBReleased: 05 March, 2012
Download: http://compbio.cs.toronto.edu/savant/dist/v1_3_1/mac/Savant%20Genome%20Browser%201.3.1.pkg
Apollo Genome Annotation Curation Tool 1.1Berkeley Bioinformatics and Ontologies Project

Apollo is a genome annotation viewer and editor. It was developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical ...

Platform: WindowsBusiness- Math & Scientific Tools
License: FreewareSize: 28.1 MBReleased: 21 March, 2012
Download: http://apollo.berkeleybop.org/current/installers/Apollo_windows_with_jre.exe
NCBI Genome Workbench 2.5.0www.ncbi.nlm.nih.gov

NCBI Genome Workbench is an integrated software for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data. Sequence data analysis made easy.Genome Workbench can display sequence data in many ways, including graphical sequence views, ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 20.9 MBReleased: 21 May, 2013
Download: http://www.ncbi.nlm.nih.gov
Argo Genome Browser 1.0.31www.broadinstitute.org

View genome files with this tool. Argo offer users a software to help you visualize and manually annotate whole genomes.
Argo Features:
1. Display of sequence and annotation tracks (from FASTA, Genbank, GFF, BLAST, BED, Wiggle (WIG), and Genscan files)
2. Extensive customization options
3. Interactive zoom from megabase to nucleotide ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 25.4 MBReleased: 13 January, 2013
Download: http://www.broadinstitute.org
Gaggle Genome Browser 0.9gaggle.systemsbiology.net

View genome data with this application. Gaggle Genome Browser is an open source program tool for visualizing high-density data plotted against coordinates on the genome. Tiling arrays, ChIP-chip, and high-throughput sequencing are a few potential use-cases. The genome browser is designed to gracefully handle large datasets, allow easy import of user ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 1.2 KBReleased: 04 March, 2013
Download: http://gaggle.systemsbiology.net/docs
3D Genome Tuner 2.1.1dgenometuner.sourceforge.net

Genome analysis made easy. 3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a strong tool in genome studies and demonstrations.Requirements:
* Java

Platform: WindowsGraphic Apps- Other
License: FreewareSize: 4.1 MBReleased: 02 January, 2013
Download: http://dgenometuner.sourceforge.net
Track Worker 1.0www.wjc.ku.dk

Ease your work with UCSC genome browser tracks. Track Worker help you work with tracks for the UCSC genome browser.Requirements:
* Java

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 666 BReleased: 19 January, 2013
Download: http://www.wjc.ku.dk
Wilhelm Johannsen - Tommerup - Niels Tommerup - Genome
Genome Explorer 1.0cbr.jic.ac.uk

Genome Explorer offer users a single interface for some useful bioinformatics tools.
It provides additional functionality for searching sequence data (for particular groups of nucleotides or amino acids) and editing multiple sequence alignments.Requirements:
* Java

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 2.5 MBReleased: 01 April, 2013
Download: http://cbr.jic.ac.uk
Bioinformatics - Computational Biology - Computational - Analysis
mRNA by SNP Browser 1.0Center for Statistical Genetics

“mRNA by SNP Browser” is an interactive package that provides graphical overviews of whole-genome association studies of datasets with very rich phenotypic information, such as global surveys of gene expression. The software incorporates a generic eQTL database and provides a graphic interface for browsing association between 54,675 ...

Platform: WindowsBusiness- Math & Scientific Tools
License: FreewareSize: 489.3 MBReleased: 22 April, 2012
Download: http://www.sph.umich.edu/csg/liang/asthma/mRNA_bySNP_browser_v1.0.1.exe
gwama 1.4WTCHG

GWAMA (Genome-Wide Association Meta Analysis) software to perform meta-analysis of the results of GWA studies of binary or quantitative phenotypes. Fixed- and random-effect meta-analyses are performed for both directly genotyped and imputed SNPs using estimates of the allelic odds ratio and 95% confidence interval for binary traits, and estimates of ...

Platform: WindowsDevelopment- Other
License: FreewareSize: 1.6 MBReleased: 19 March, 2012
Download: http://www.well.ox.ac.uk/GWAMA/gwama_win1.4.zip
EagleView 2.2Weichun Huang

EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism ...

Platform: WindowsEducation- Science
License: FreewareSize: 1.8 MBReleased: 05 March, 2012
Download: http://bioinformatics.bc.edu/marthlab/EagleViewMS_Windows_.28XP_or_Vista.29_Distribution
AssociationViewer 2.0associationviewer.vital-it.ch

Analyze the genome with this tool. AssociationViewer is a Java software used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.AssociationViewer Features:
1. Display SNPs and their ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 3.2 MBReleased: 16 May, 2013
Download: http://associationviewer.vital-it.ch
GenomeView 1912 Betagenomeview.sourceforge.net

View genome files with this tool. GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.GenomeView Features:
1. Genome browsing
2. Short read alignment visualization

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 3.2 MBReleased: 28 April, 2013
Download: http://genomeview.org
ped2raw 1.0ped2raw.sourceforge.net

Convert PED genome file fast and easy. ped2raw convert PED genome file into RAW SNP format. Creates multiple files per person and it offers support for big files.SYNOPSIS
ped2raw <input_file>
ped2raw -i <input_file> -s <snips_file>
ped2raw <input_file> -s <snips_file>OPTIONS:
-i Input PED file (filename ...

Platform: WindowsSystem Utilities- File & Disk Management
License: FreewareSize: 37.8 KBReleased: 11 December, 2012
Download: http://ped2raw.sourceforge.net
Mgenome 1.0xungulab.com

Genome analysis made easy. This software is designed to find the optimal trees for multiple genome rearrangement by signed reversals. The problem is modeled as: For a given collection of genomes represented by signed permutations on genes, find a tree to connect the given genomes by reversal paths such that the number of all signed reversals is minimized.

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 17.0 KBReleased: 04 April, 2013
Download: http://xungulab.com
Genome2D 3.17molgen.biol.rug.nl

Genome2D visualizes a bacterial genome with all its individual genes on a single computer screen genome enables quick identification of biologically relevant information such as gene orientation, operon structure, transcriptional terminators or regulator binding sites. Bacterial genome analysis made easy.Using a simple input file subsets of genes can ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 13.0 MBReleased: 20 December, 2012
Download: http://molgen.biol.rug.nl
ACT (The Artemis Comparison Tool) 9.0www.sanger.ac.uk

It is based on the program for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.ACT is freely available to anyone. Please acknowledge us if you ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 8.7 MBReleased: 12 March, 2013
Download: http://www.sanger.ac.uk
Cambridge - Bioinformatics - Genome Sequencing - Research Institute
GenomeComp 1.3www.mgc.ac.cn

Genome wide sequence analysis made easy. GenomeComp is a DNA sequence comparison tool and graphical user interface (GUI) viewer implemented in Perl/Tk. It can read one, two or three input sequences in either of FASTA, GENBANK or EMBL format, then it runs the external software BLASTN or MegaBlast to do the comparison between paired sequences in background.

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 1.2 MBReleased: 17 March, 2013
Download: http://www.mgc.ac.cn
MOH Key Laboratory Of Systems Biology Of Pathogens - Institute Of Pathogen Biology IPB - Chinese - Academy
Easyfig 2.0easyfig.sourceforge.net

Genome analysis made easy. Easyfig is a python software for creating linear comparison figures and graphs of multiple genomic loci with and easy to use graphical interface. BLAST comparisons beween multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualised and interactively coloured, enabling a ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 8.0 MBReleased: 01 April, 2013
Download: http://easyfig.sourceforge.net
GPS (Genome Positioning System) 1.0cgs.csail.mit.edu

TThe Genome Positioning System (GPS) is a utility tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution.GPS has 3 main features:
1. Achieve high spatial resolution on predicting binding events
2. Resolve closely ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 25.3 MBReleased: 18 April, 2013
Download: http://cgs.csail.mit.edu
GS2 1.8www.well.ox.ac.uk

Analyze genome association studies with this tool. GS2 help you analyze and visualize whole genome association studies. With recent advances in the efficiency of high-throughput single nucleotide polymorphism (SNP) genotyping technology, genome-wide association studies are now routinely undertaken with the sample sizes necessary to detect the modest ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 31.2 MBReleased: 21 January, 2013
Download: http://www.well.ox.ac.uk
JCoast 1.6 Beta 3www.jcoast.net

JCoast is a next-generation program solution for the exploration, mining and comparison of your genome and metagenome projects. Based on a set of predicted and automatically annotated ORFs (a genome or metagenome) it acts as a window into these preprocessed data which does not only allow to view the initial results but also facilitates improved annotation ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 778 BReleased: 23 January, 2013
Download: http://www.jcoast.net
Jcoast - Genome - Metagenome - Browser
GenomeSlicer 1.1genomeslicer.sourceforge.net

GenomeSlicer facilitates subsequence extraction from fasta format genome sequences. A graphical tool for Microsoft Windows which extracts relevant sub-sequences from Fasta or Genbank format sequence files. GenomeSlicer can return targeted coding sequences (genes), variable regions upstream or downstream of genes, as well as sub-sequences specified ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 2.1 MBReleased: 22 January, 2013
Download: http://genomeslicer.sourceforge.net
CisGenome 1.2www.biostat.jhsph.edu

CisGenome is an integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis, help you tille array, ChIP-seq, genome and cis-regulatory element analysis.

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 4.1 MBReleased: 03 February, 2013
Download: http://www.biostat.jhsph.edu
RetroMap 0.021www.burchsite.com

Helps characterize LTR retroelements on a genome scale. RetroMap assist you in the analysis of LTR retroelements. It is not particularly outstanding for comprehensive identification of elements found in highly nested contexts.
Only the most internal element of those which are nested is likely to be identified as a complete element. The other elements ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 1.4 MBReleased: 11 December, 2012
Download: http://www.burchsite.com
GEvolutionS 1.0bibiserv.techfak.uni-bielefeld.de

Genome evolution simulation software. GEvolutionS can simulates an evolutionary Genome rearrangement scenario with different genome rearrange operations. It operates on the most general model of genomes with a mixed collection on linear and circular genomes.
The simulation process includes all classical rearrangement operations such as dcj, fissions, ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 708 BReleased: 17 March, 2013
Download: http://bibiserv.techfak.uni-bielefeld.de
GeneNotes 1.0Brandeis University and Stanford University

In genome-wide profiling project, researchers usually select many sets of genes (or ESTs) for further investigation based on the computational analyses of the experimental data. For example, a set of genes is selected because they are clustered together based on their mRNA levels. To generate or support biologically meaningful hypotheses, researchers ...

Platform: WindowsNetwork & Internet- Other
License: FreewareSize: 44.0 MBReleased: 03 February, 2012
Download: http://combio.cs.brandeis.edu/GeneNotes/Download/GeneNotes.msi
HarvEST Brachypodium 0.5Steve Wanamaker and Timothy Close



Initial development of HarvEST:Brachypodium was funded by the USDA/CSREES Plant Genome program.

Platform: WindowsBusiness- Other
License: FreewareSize: 26.4 MBReleased: 01 April, 2012
Download: http://harvest.ucr.edu/HBrachy054.exe


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