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http://tmaj.pathology.jhmi.edu/
Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
Proper citation: TMAJ (RRID:SCR_005601) Copy
http://maq.sourceforge.net/maqview.shtml
A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy.
Proper citation: Maqview (RRID:SCR_005632) Copy
http://staden.sourceforge.net/
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
Proper citation: Staden Package (RRID:SCR_005629) Copy
http://snp-magma.sourceforge.net
Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem.
Proper citation: MAGMA (RRID:SCR_005757) Copy
http://brainnetworks.sourceforge.net
Brain Networks: Code to perform network analysis on brain imaging data.
Proper citation: Brain Networks (RRID:SCR_005841) Copy
http://estscan.sourceforge.net/
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics.
Proper citation: ESTScan (RRID:SCR_005742) Copy
http://sourceforge.net/projects/bless-ec/
Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.
Proper citation: BLESS (RRID:SCR_005963) Copy
https://compbio.dfci.harvard.edu/predictivenetworks//
A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model.
Proper citation: Predictive Networks (RRID:SCR_006110) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://sourceforge.net/apps/mediawiki/cdao/
A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science
Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy
http://htsvipr.sourceforge.net/
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
Proper citation: vipR (RRID:SCR_010685) Copy
http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks
Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).
Proper citation: FindPeaks (RRID:SCR_010857) Copy
http://contra-cnv.sourceforge.net/
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Proper citation: CONTRA (RRID:SCR_010814) Copy
http://svdetect.sourceforge.net/Site/Home.html
Software 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 identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Proper citation: SVDetect (RRID:SCR_010812) Copy
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Proper citation: Celera assembler (RRID:SCR_010750) Copy
http://dnptrapper.sourceforge.net/
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Proper citation: DNPTrapper (RRID:SCR_010981) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
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