PGDSpider statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PGDSpider
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Tool usage distribution map

This map represents all the scientific publications referring to PGDSpider per scientific context
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Associated diseases

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Popular tool citations

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Protocols

PGDSpider specifications

Information


Unique identifier OMICS_17989
Name PGDSpider
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format PGD, Arlequin, BAM, BAPS, BATWING, BCF, EIGENSOFT, XMFA, FASTA, FASTQ, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, Immanc, IM, IMa2, MEGA, MIGRATE, MSA, NewHybrids, NEXUS, ONeSAMP, PED, PHYLIP, SAM, fastSTRUCTURE, VCF, CONVERT, HGDP, HGDP-CEPH, MAF
Output format BAMOVA, Bayenv, FDist2, GESTE, KML, MSVar, Strcturama, PGD, Arlequin, BAM, BAPS, BATWING, BCF, EIGENSOFT, XMFA, FASTA, FASTQ, FSTAT, GDA, GENELAND, GENEPOP, GENETIX, Immanc, IM, IMa2, MEGA, MIGRATE, MSA, NewHybrids, NEXUS, ONeSAMP, PED, PHYLIP, SAM, fastSTRUCTURE, VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.1.1.0
Stability Stable
Requirements
JRE
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Heidi Lischer

Additional information


http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%202-1-1-0.pdf

Publication for PGDSpider

PGDSpider citations

 (51)
library_books

Complex signatures of genomic variation of two non model marine species in a homogeneous environment

2018
BMC Genomics
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] genotyped individuals. GenePop files were further edited using custom Perl script, to merge all contigs and identify locus positions.The edited GenePop files were converted into Bayescan files using PGDSpider2 v2.1.03 []. The first outlier detection method, Bayescan v.2.1 [], was run with 20 pilot runs, 10,000 iterations and a burn-in of 50,000, and 55,000 reversible-jump MCMC chains, using a pri […]

call_split

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

2018
Ecol Evol
PMCID: 5938456
PMID: 29760905
DOI: 10.1002/ece3.4017
call_split See protocol

[…] calls are presented here for clarity (mismatch thresholds of 2 bp, minimum stack and final locus depths of 5 and 10, respectively). Conversion of file formats from STACKS output files was made using PGDSpider v. 2.0.5.1 (Lischer & Excoffier, ). Possible outlier loci were identified using Bayescan v. 2.1 (Foll & Gaggiotti, ) with a burn‐in of 5 × 104 followed by a total of 1 × 106 iterations. Loci […]

call_split

Oat evolution revealed in the maternal lineages of 25 Avena species

2018
Sci Rep
PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4
call_split See protocol

[…] ample were calculated in Microsoft Excel®. To facilitate the phylogenetic analysis below, we also converted each FASTA SNP data set to the related NEXUS or PHYLIP formats using either ClustalX 2.0 or PGDSpider v2.1.0.0. […]

call_split

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

2018
Ann Bot
PMCID: 5786241
PMID: 29325077
DOI: 10.1093/aob/mcx129
call_split See protocol

[…] uding all 34 individuals and the second omitting the two outgroup accessions (Steveniella and Serapias). The filtered vcf files were converted to phylip format by concatenating the SNP positions with PGDSpider v.2.0.8.2 (), summarizing heterozygosities as IUPAC ambiguities.The ingroup-only file was further used to produce a phylogenetic network in SPLITSTREE v.4.3.11 (). Splits were created from u […]

library_books

Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

2017
Ecol Evol
PMCID: 5756825
PMID: 29321894
DOI: 10.1002/ece3.3583

[…] v0.1.14 (Danecek et al., ) to select for bi‐allelic SNPs with a maximum missing genotype of 10% and a minor allele frequency of 5%. We reformatted the resulting variant call format file (.vcf) using pgdspider v2.0.9.2 (Lischer & Excoffier, ) for the structure v2.3.4 (Pritchard, Stephens, & Donnelly, ) and F ST outlier analyses.We used the tandem repeat finder trf v4.09b (Benson, ) to annotate the […]

library_books

Genetic Diversity and Connectivity in Maurolicus muelleri in the Bay of Biscay Inferred from Thousands of SNP Markers

2017
Front Genet
PMCID: 5712365
PMID: 29234350
DOI: 10.3389/fgene.2017.00195

[…] SNPs with MAF larger than 0.05 and a genotyping rate larger than 0.9 were selected for population structure analyses. The obtained genotype dataset was exported to Structure and Genepop formats using PGDSpider version 2.0.8.3 (). […]


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PGDSpider institution(s)
Computational and Molecular Population Genetics (CMPG) laboratory, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
PGDSpider funding source(s)
Supported by Swiss National Science Foundation (grant No 3100A0- 126074).

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