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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…
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Stacks
Desktop
Web
Server

Stacks

Builds genetic maps and conducts population genomics and phylogeography. Stacks…

Builds genetic maps and conducts population genomics and phylogeography. Stacks is a software system developed to work with restriction enzyme-based data, such as RAD-seq. The software produces core…

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PyRAD
Desktop

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…

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Rtd
Desktop

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…

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RADtools
Desktop

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…

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AMF
Desktop

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…

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RADIS
Desktop

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…

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Rainbow
Desktop

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…

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SimRAD
Desktop

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.…

RADami
Desktop

RADami

A partitioned restriction-site associated DNA (RAD) visualization method to…

A partitioned restriction-site associated DNA (RAD) visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate…

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AftrRAD
Desktop

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…

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dDocent
Desktop

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…

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RADtyping
Desktop

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.

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REDseq
Desktop

REDseq

Includes functions to build restriction enzyme cut site (RECS) map, and…

Includes functions to build restriction enzyme cut site (RECS) map, and distributes mapped sequences on the map with five different approaches. REDseq is a Bioconductor package for building genomic…

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PredRAD
Desktop

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…

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restrict
Desktop

restrict

Reports restriction enzyme cleavage sites in a nucleotide sequence. restrict…

Reports restriction enzyme cleavage sites in a nucleotide sequence. restrict scans one or more nucleotide sequences for cut sites for a supplied set of restriction enzymes. The user can specify one…

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recoder
Desktop

recoder

Finds restriction enzyme sites in a nucleotide sequence which can be removed…

Finds restriction enzyme sites in a nucleotide sequence which can be removed without changing the translation. recoder scans a nucleotide sequence for restriction sites for a supplied set of…

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silent
Desktop

silent

Finds restriction sites to insert (mutate) with no translation change. silent…

Finds restriction sites to insert (mutate) with no translation change. silent scans a nucleotide sequence for restriction sites for a supplied set of restriction enzymes. It writes a standard EMBOSS…

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simRRLs
Desktop

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…

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RApiD
Desktop

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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