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PyRAD specifications


Unique identifier OMICS_03724
Name PyRAD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Deren A. R. Eaton

Publication for PyRAD

PyRAD citations


An optimized approach for local de novo assembly of overlapping paired end RAD reads from multiple individuals

R Soc Open Sci
PMCID: 5830760
PMID: 29515871
DOI: 10.1098/rsos.171589

[…] the second reads for assembly, and therefore the information for the first reads was lost. There are several software for the assembly of RAD data supporting PE reads, such as Stacks [,], Rainbow [], pyRAD [] and dDocent []. However, many of these tools cannot directly and fully support RPE datasets with staggered PE reads. There are many studies which did not make full use of RPE reads either for […]


Genome wide SNP data and morphology support the distinction of two new species of Kovarikia Soleglad, Fet and Graham, 2014 endemic to California (Scorpiones, Vaejovidae)

PMCID: 5904437
PMID: 29674883
DOI: 10.3897/zookeys.739.20628

[…] g Laboratory at UC Berkeley for 150-base single-end sequencing on one lane of an Illumina HiSeq4000 (combined with 10 pooled libraries in the lane).We demultiplexed and processed Illumina reads using pyRAD v2.16.1 (, ). Sequences were clustered at 90% similarity within samples using USEARCH v7.0.1090 () and aligned with MUSCLE v3.8.31 (). Error rate and heterozygosity were jointly estimated from t […]


RADpainter and fineRADstructure: Population Inference from RADseq Data

Mol Biol Evol
PMCID: 5913677
PMID: 29474601
DOI: 10.1093/molbev/msy023

[…] core Stacks populations program. A third party utility script (; last accessed February 24, 2018) also enables conversion from the format of the pyRAD and ipyrad toolkits (). Finally, our input format is a simple flat text file and we provide an example data set to enable the users of other pipelines to prepare their data. […]


Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

PMCID: 5829208
PMID: 29445022
DOI: 10.1098/rspb.2017.2732

[…] The conservative concatenated dataset generated by pyRAD consisted of 44 521 bases of sequence which contained 7879 variable sites, 5591 of which were parsimony informative, with 5.9% missing data across all taxa. Both the Bayesian and maximum likelih […]


Genome wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

PLoS One
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] t the genotypes and the read depth per site for every individual sample in the dataset. Given that one of the main aims of this study is the species delimitation of B. tabaci cryptic complex, we used PyRAD, an additional pipeline developed specifically for RADseq data looking at introgression and phylogenetic inferences. The advantage of this pipeline is that it takes into account the insertions a […]


Integrating restriction site associated DNA sequencing (RAD seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

Ann Bot
PMCID: 5786241
PMID: 29325077
DOI: 10.1093/aob/mcx129

[…] bp for the pair-reads after removing the barcode sequence. In total, 8.1 million pairs (17.6 % of the total) could be successfully extended with FLASH up to a length of 180 bp. After clustering using PyRAD, a total of 127 983 bp over 751 contigs were retained as a pseudo-reference for calling variants. The raw variant file contained 16 758 SNPs and 3022 indels. After filtering with the settings sp […]

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PyRAD institution(s)
Committee on Evolutionary Biology, University of Chicago, IL, USA; Botany Department, Field Museum of Natural History, IL, USA
PyRAD funding source(s)
This research was supported by a National Science Foundation Dissertation Improvement Grant (DEB-1110598).

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