RAD sequencing data analysis bioinformatics software tools
RAD markers were first implemented using microarrays (Miller et al., 2007) and later adapted for NGS (Baird et al., 2008). RAD-seq could generate a genome-wide density of genetic markers. RAD-seq has been used to study population differentiation and selection (Emerson et al.,…
Desktop app
G T A T C G C T A dDocent dDocent

dDocent

Designed to process individually barcoded Restriction-site associated DNA…

Designed to process individually barcoded Restriction-site associated DNA sequencing (RADseq) data (with double cut sites) into informative single nucleotide polymorphisms (SNPs)/Indels for…

Desktop app
RADami RADami

RADami

A partitioned RAD visualization method to investigate the possibility that…

A partitioned RAD visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage…

Desktop app
G T A T C G C T A AgroMarker Finder AgroMarker Finder

AMF AgroMarker Finder

A GUI software for providing graphical user interface (GUI) to facilitate the…

A GUI software for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. AMF integrates sophisticated…

Desktop app
G T A T C G C T A PyRAD PyRAD

PyRAD

A pipeline to assemble de novo RADseq loci with the aim of optimizing coverage…

A pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets. PyRAD uses a wrapper around an alignment-clustering algorithm, which allows for indel…

Desktop app
G T A T C G C T A RADtools RADtools

RADtools

A toolkit for processing and analysing RAD sequencing data. The tools are…

A toolkit for processing and analysing RAD sequencing data. The tools are designed to process de novo RAD data, that is, data from species without a reference genome. RADtools integrates RADpools for…

Desktop app
G T A T C G C T A analysis of RAD-seq… analysis of RAD-seq data for InterSpecific…

RADIS analysis of RAD-seq data for InterSpecific phylogeny

Automates and standardizes the analyses of RAD-seq data for phylogenetic…

Automates and standardizes the analyses of RAD-seq data for phylogenetic inference. Users of RADIS can let their raw Illumina data be processed up to phylogenetic tree inference, or stop (and…

Desktop app
G T A T C G C T A simRRLs simRRLs

simRRLs

A program to simulate raw RADseq-like sequence data with options to modify…

A program to simulate raw RADseq-like sequence data with options to modify tree, population, sequencing, and formatting parameters. Its main purpose is for testing assembly methods on raw data. The…

Desktop app
G T A T C G C T A PredRAD PredRAD

PredRAD

For the design of a study using RAD-seq, or a related methodology, there are…

For the design of a study using RAD-seq, or a related methodology, there are two general fundamental questions that researchers face: i) what is the best restriction enzyme to use to obtain a desired…

Desktop app
G T A T C G C T A SimRAD SimRAD

SimRAD

An R package that performs in silico restriction enzyme digests and fragment…

An R package that performs in silico restriction enzyme digests and fragment size selection as implemented in most restriction site associated DNA polymorphism and genotyping by sequencing methods.…

Desktop app
G T A T C G C T A AftrRAD AftrRAD

AftrRAD

Assembles and genotypes RADseq data, and outputs these data in various formats…

Assembles and genotypes RADseq data, and outputs these data in various formats for downstream analyses. AftrRAD is able to accurately assemble loci, while accounting for indel variation among…

Desktop app
G T A T C G C T A RADtyping RADtyping

RADtyping

A user-defined perl procedure for performing de novo RAD genotyping in mapping…

A user-defined perl procedure for performing de novo RAD genotyping in mapping populations.

Desktop app
G T A T C G C T A Rtd Rtd

Rtd

Reference-free ddRADseq analysis tools. Rtd includes a custom combinatorial…

Reference-free ddRADseq analysis tools. Rtd includes a custom combinatorial indexing method, and accompanies software tools to facilitate genotyping across large numbers (hundreds or more) of…

Desktop app
G T A T C G C T A Rainbow Rainbow

Rainbow

Provides an ultra-fast and memory-efficient solution to clustering and…

Provides an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a…

Desktop app
G T A T C G C T A Stacks Stacks

Stacks

Developed to work with restriction enzyme-based data, such as RAD-seq, for the…

Developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

Desktop app
G T A T C G C T A RApiD RApiD

RApiD

A method for de novo assembly of paired-end RAD-seq data in order to produce…

A method for de novo assembly of paired-end RAD-seq data in order to produce extended contigs flanking a restriction site.

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