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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
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
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
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
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
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
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
Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.
Proper citation: NIDB - Neuroinformatics Database (RRID:SCR_002488) Copy
http://scralyze.sourceforge.net
A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.
Proper citation: SCRalyze (RRID:SCR_002542) Copy
http://andestools.sourceforge.net/
Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.
Proper citation: ANDES (RRID:SCR_002791) Copy
http://sourceforge.net/projects/glprobs/
Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.
Proper citation: GLProbs (RRID:SCR_002739) Copy
http://sourceforge.net/projects/bio-rainbow/
Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.
Proper citation: Rainbow (RRID:SCR_002724) Copy
A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.
Proper citation: rDock (RRID:SCR_002838) Copy
http://sourceforge.net/projects/fas-dpd/
Software program to design degenerate primers for PCR.
Proper citation: FAS-DPD (RRID:SCR_003068) Copy
http://sourceforge.net/projects/salt1/
Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.
Proper citation: SALT (RRID:SCR_003187) Copy
http://sourceforge.net/projects/xorro-overlap/
Efficient paired-read overlap software program for use with Illumina sequencing.
Proper citation: XORRO (RRID:SCR_003181) Copy
http://compbio.cs.sfu.ca/software-novelseq
Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
Proper citation: NovelSeq (RRID:SCR_003136) Copy
http://mrcanavar.sourceforge.net/
Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.
Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy
http://sourceforge.net/projects/primerdesigner/
High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.
Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy
http://sourceforge.net/projects/saskprimerfs/
Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.
Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy
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