Tools   Select Another Resource Report Type

http://knowtator.sourceforge.net/

A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.

Proper citation: Knowtator (RRID:SCR_012099) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pb-jelly/

Software that automates the finishing process using long sequence reads in a reference-guided assembly process.

Proper citation: PBJelly (RRID:SCR_012091) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dical-ibd/

Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences.

Proper citation: diCal-IBD (RRID:SCR_012111) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ionwinze/

Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures.

Proper citation: Ionwinze (RRID:SCR_012115) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/genosight/

An adaptive imaging cytometry software environment.

Proper citation: GenoSIGHT (RRID:SCR_012119) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/isdtool/files/ISDTool-2.0/

Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV.

Proper citation: ISDTool (RRID:SCR_012125) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngopt/

Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.

Proper citation: A5-miseq (RRID:SCR_012148) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ec2kegg/

A perl-based package to perform comparative analysis of metabolic pathways between two organisms.

Proper citation: EC2KEGG (RRID:SCR_012127) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnvcapseq/

Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing.

Proper citation: cnvCapSeq (RRID:SCR_012126) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ealps/

Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).

Proper citation: eALPS (RRID:SCR_012130) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/plek/

An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.

Proper citation: PLEK (RRID:SCR_012132) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ldx/

A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.

Proper citation: LDx (RRID:SCR_012131) Copy   

•   Source: SciCrunch Registry

http://pprospector.sourceforge.net/

A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.

Proper citation: PrimerProspector (RRID:SCR_012136) Copy   

•   Source: SciCrunch Registry

http://musite.sourceforge.net/

A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.

Proper citation: Musite (RRID:SCR_012141) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phosphosite/

A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.

Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnv/

Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

Proper citation: CNV Workshop (RRID:SCR_012635) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/krona/home/krona/

Software that allows hierarchical data to be explored with zoomable pie charts.

Proper citation: Krona (RRID:SCR_012785) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar

Accurate error-correction of amplicon pyrosequences.

Proper citation: Acacia (RRID:SCR_012896) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ibdld/

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

Proper citation: IBDLD (RRID:SCR_013043) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/solsnp/

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

Proper citation: SolSNP (RRID:SCR_013045) Copy   

•   Source: SciCrunch Registry