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http://www.pathxl.com/pathxl-research/pathxl-tma

Tissue microarray (TMA) Software used for Biomarker Discovery that allows TMA experiments to be performed anytime, anywhere, reducing administrative costs and time. It is designed to support TMA scoring workflow and allows configuration of experiments in minutes. Access and view clinical metadata, the TMA core, scoring criteria and the TMA map all on a single interface.

Proper citation: PathXL TMA (RRID:SCR_005596) Copy   

•   Source: SciCrunch Registry
  

http://www.dnabaser.com/download/chromatogram-explorer/

A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware.

Proper citation: DNA Chromatogram Explorer (RRID:SCR_005585) Copy   

•   Source: SciCrunch Registry
  

http://clip.med.yale.edu/SHM

A targeting model that defines where mutations occur (by specifying the relative rates at which DNA motifs in the Ig sequence are mutated), and a nucleotide substitution model that defines the resulting mutation (by specifying the probability of each base mutating to each of the other three possibilities as a function of the surrounding bases).

Proper citation: Models of SHM Targeting and Substitution (RRID:SCR_005250) Copy   

•   Source: SciCrunch Registry
  

http://rp-www.cs.usyd.edu.au/~yangpy/software/MFGE.html

A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.

Proper citation: MF-GE (RRID:SCR_003509) Copy   

•   Source: SciCrunch Registry
  

http://omicsoft.com/osa/

A fast and accurate alignment tool for RNA-Seq data.

Proper citation: Omicsoft Sequence Aligner (RRID:SCR_005270) Copy   

•   Source: SciCrunch Registry
  

http://www.timelogic.com/catalog/799/velocimapper

Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives.

Proper citation: VelociMapper (RRID:SCR_005262) Copy   

•   Source: SciCrunch Registry
  

http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry
  

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry
  

http://realtimegenomics.com/products/variant-1.0

The product line encompasses distinct products for the specific needs of clinical research, saving time and money while allowing customers to focus on the answers they need most.

Proper citation: RTG Variant (RRID:SCR_010805) Copy   

•   Source: SciCrunch Registry
  

http://www.premierbiosoft.com/dnamicroarray/index.html

Oligo and cDNA Microarray Design Software that designs thousands of primers and probes for oligo and cDNA microarrays in seconds.

Proper citation: Array Designer (RRID:SCR_010960) Copy   

•   Source: SciCrunch Registry
  

http://www.genomics.agilent.com/en/Microarray-Data-Analysis-Software/GeneSpring-GX/?cid=AG-PT-130&tabId=AG-PR-1061

Powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.

Proper citation: GeneSpring GX (RRID:SCR_010972) Copy   

•   Source: SciCrunch Registry
  

http://www.exiqon.com/mirna-array-software

Software for fast and accurate analysis of miRCURY LNA microRNA Array data.

Proper citation: miRCURY LNA microRNA Array Analysis Software (RRID:SCR_010952) Copy   

•   Source: SciCrunch Registry
  

http://realtimegenomics.com/products/metagenomics-1.0

Delivers comprehensive shotgun metagenomics sequence analysis for accurate species frequency composition and protein searching.

Proper citation: RTG Metagenomics (RRID:SCR_011949) Copy   

•   Source: SciCrunch Registry
  

http://www.genomatix.de/solutions/index.html

With their unique combination of proprietary algorithms and comprehensive data background, all our solutions do more than enable you to efficiently and effectively analyze and interpret biological data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Genomatix Solutions (RRID:SCR_011855) Copy   

•   Source: SciCrunch Registry
  

http://sbcb.bioch.ox.ac.uk/kdb/

A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations.

Proper citation: Potassium Channel Database (RRID:SCR_011960) Copy   

•   Source: SciCrunch Registry
  

http://www.meta-analysis.com/index.php

A software package to do meta-analysis which works in a spreadsheet interface and also provides forest plots, which are useful for visualizing between-study heterogeneity.

Proper citation: CMA (RRID:SCR_012779) Copy   

•   Source: SciCrunch Registry
  

http://www.phylotree.org/

A phylogenetic tree of global human mitochondrial DNA variation, based on both coding- and control-region mutations, and including haplogroup nomenclature.

Proper citation: PhyloTree.org (RRID:SCR_012948) Copy   

•   Source: SciCrunch Registry
  

http://www.microbesonline.org/fasttree/

Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution.

Proper citation: FastTree (RRID:SCR_015501) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/phytools/index.html

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry
  

http://www.genome.gov/27549169

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV

Proper citation: NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects (RRID:SCR_003205) Copy   

•   Source: SciCrunch Registry