R

R is a free software environment for statistical computing and graphics.

Easy Copy Number. EaCoN aims to be an all-packed in, user-friendly solution to perform relative or absolute copy-number analysis for multiple sources of data, with three different segmenters available (and corresponding three copy-number modelization methods)

Statistical Analysis of RNA-Seq data

STITCH - Sequencing To Imputation Through Constructing Haplotypes

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

Chromosome-level scaffolding using multiple references

Fast reference-guided genome assembly scaffolding

RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations.

RattleSNP is an open-source, scalable, modular and traceable Snakemake pipeline, able to launch mapping, SNP calling and generate report to help user of filtering

Raven is an assembler for raw reads generated by the third generation sequencing.

Phylogenetics - Randomized Axelerated Maximum Likelihood.

RAxML Next Generation: faster, easier-to-use and more flexible

Naive Bayesian classifier that can rapidly and accurately provide taxonomic assignments from domain to genus

Reads2SN by PopPhyl

A toolbox for improving population genomes.

Relion is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM)

RelocaTE2: a high resolution transposable element insertion sites mapping tool for population resequencing.

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

RepeatModeler is a de-novo repeat family identification and modeling package.

The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale.

software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM)

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

Toolkit to perform regulatory genomics data analysis

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.

rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.

Fast, efficient RNA-Seq metrics for quality control and process optimization

Rapid large-scale prokaryote pan genome analysis

RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs). Because RiPP precursor peptides are small and often evade annotation in sequence databases, RODEO can also manually translate small ORFs (open reading frames). A combination of support vector machine (SVM) learning and motif analysis can be used to scan unannotated intergenic regions for RiPP precursors.

The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute's Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.

RNA-seq QC Package

RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server

RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation

Standalone version of dbCAN annotation tool for automated CAZyme annotation