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http://bioinformatics.ua.pt/software/mfcompress/

A compression tool for FASTA and multi-FASTA files.

Proper citation: MFCompress (RRID:SCR_009301) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.research.nicta.com.au/software/rlz/

Optimized relative Lempel-Ziv compression of genomes.

Proper citation: RLZ (RRID:SCR_009420) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz

A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GReEn (RRID:SCR_009264) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/ISRNA/

An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ISRNA (RRID:SCR_009565) Copy   

•   Source: SciCrunch Registry

http://users-mb.au.dk/pmgrp/downloads.php

A pipeline for small RNA-seq data analysis.

Proper citation: shortran (RRID:SCR_009636) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

http://www.allseq.com/default.aspx

Free online tools to find the best Sequencing Service provider for your project.

Proper citation: AllSeq (RRID:SCR_010053) Copy   

•   Source: SciCrunch Registry

http://dna.engr.uconn.edu/?page_id=105

Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.

Proper citation: IsoEM (RRID:SCR_009993) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/bitseq/

A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.

Proper citation: BitSeq (RRID:SCR_009904) Copy   

•   Source: SciCrunch Registry

http://bioen-compbio.bioen.illinois.edu/TrueSight/

Self-training Algorithm for Splice Junction Detection using RNA-seq.

Proper citation: TrueSight (RRID:SCR_009835) Copy   

•   Source: SciCrunch Registry

http://hkbic.cuhk.edu.hk/software/abmapper

A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.

Proper citation: ABMapper (RRID:SCR_010242) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/GLAD.html

Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

Proper citation: GLAD (RRID:SCR_001284) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bycom/

A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output.

Proper citation: Bycom (RRID:SCR_000659) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/VennDiagram/

Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Proper citation: VennDiagram (RRID:SCR_002414) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

https://omictools.com/prolinks-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.

Proper citation: ProLinks Database of Functional Linkages (RRID:SCR_003185) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/metaMA/

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

Proper citation: metaMA (RRID:SCR_000408) Copy   

•   Source: SciCrunch Registry

Issue

https://reich.hms.harvard.edu/software

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Proper citation: Eigensoft (RRID:SCR_004965) Copy   

•   Source: SciCrunch Registry