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http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pyqpcr/

A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

Proper citation: pyQPCR (RRID:SCR_000471) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/popbam/

A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

Proper citation: POPBAM (RRID:SCR_000464) Copy   

•   Source: SciCrunch Registry

http://drfast.sourceforge.net/

A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.

Proper citation: drFAST (RRID:SCR_000586) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://brainnetworks.sourceforge.net

Brain Networks: Code to perform network analysis on brain imaging data.

Proper citation: Brain Networks (RRID:SCR_005841) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://buridan.sourceforge.net/

Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.

Proper citation: Centroid Trajectory Analysis (RRID:SCR_006331) Copy   

•   Source: SciCrunch Registry

http://denovoassembler.sourceforge.net/

Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.

Proper citation: Ray Meta (RRID:SCR_011918) Copy   

•   Source: SciCrunch Registry

http://uc-echo.sourceforge.net/

Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.

Proper citation: ECHO (RRID:SCR_011851) Copy   

•   Source: SciCrunch Registry

http://tagcleaner.sourceforge.net/

A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.

Proper citation: TagCleaner (RRID:SCR_011846) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirplant/

A user-friendly plant miRNA prediction tool.

Proper citation: miRPlant (RRID:SCR_012105) Copy   

•   Source: SciCrunch Registry

http://pypedal.sourceforge.net/

A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.

Proper citation: PyPedal (RRID:SCR_012104) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/simulatepcr/

Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.

Proper citation: Simulate PCR (RRID:SCR_012106) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sat-assembler/

A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.

Proper citation: SAT-Assembler (RRID:SCR_012108) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fingerid/

A metabolite identification software using tandem mass spectrometry and kernel methods.

Proper citation: FingerID (RRID:SCR_012077) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protrac/

A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.

Proper citation: proTRAC (RRID:SCR_012078) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/netmode/

Fast motif detection algorithm for subgraph size no more than 6.

Proper citation: NetMODE (RRID:SCR_012085) Copy   

•   Source: SciCrunch Registry