PGDSpider protocols

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PGDSpider statistics

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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

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Versioning


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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 in pipelines

 (7)
2017
PMCID: 5395438
PMID: 28428843
DOI: 10.1002/ece3.2872

[…] missing >5% of genotypes were removed. finally, only one snp per rad tag was retained to remove the effects of physical linkage. the resulting panel was converted for subsequent analyses using pgdspider v2.0.8.3 (lischer & excoffier, ) and the r package genepopedit (stanley, jeffery, wringe, dibacco, & bradbury, 2017)., multiple approaches were used to identify loci putatively […]

2017
PMCID: 5519588
PMID: 28729652
DOI: 10.1038/s41598-017-06085-3

[…] more snps to be recovered within the ingroup, which resulted in 430 high quality informative snps shared across all pocillopora libraries. the vcf file was converted to binary nexus format using pgdspider v.2.0.9.1. in beauti all taxa were treated as distinct species and the priors, u and v, were calculated from the data. in beast 2.3.2 the mcmc chain was run for 3,000,000 generations, […]

2017
PMCID: 5701561
PMID: 29181279
DOI: 10.7717/peerj.4077

[…] = 11, gap extension penalty = 1, length of initial exact match (word size) = 6 and scoring matrix = blosum62 using blastx 2.2.32 + ()., the stacks exported genepop dataset was also reformatted with pgdspider version 2.0.5.2 () to a geste file. the method of was performed using bayescan 2.0 (http://www-leca.ujf-grenoble.fr/logiciels.html). for each locus, the probability […]

2016
PMCID: 4801390
PMID: 26999359
DOI: 10.1371/journal.pone.0151651

[…] paralogs and multi-copy sites were removed based on a coverage of a standard-deviation three times higher than the mean []. vcf format files [] were converted to snp-based nexus files using pgdspider converter [] and to structure data files for every individual using the vcf-consensus tool (see also ). updated versions of the bioinformatic pipeline can be found […]

2016
PMCID: 4859572
PMID: 27152522
DOI: 10.1371/journal.pone.0154722

[…] v1.9 [, ]. then, 121 positions were randomly extracted from each of the bins 3 times and merged to create 3 datasets with equal representation of each frequency bin. these datasets were recoded with pgdspider v2.1.0.0 [] and used as input to structure. structure was run for 1,000,000 iterations with 200,000 burnin period for 6 clusters. the results were united with clumpp v1.1.2 [] […]


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PGDSpider in publications

 (47)
PMCID: 5944137
PMID: 29743012
DOI: 10.1186/s12864-018-4721-y

[…] 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 […]

PMCID: 5844911
PMID: 29523798
DOI: 10.1038/s41598-018-22478-4

[…] 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., three types of phylogenetic analysis were performed in a linux server based on cp, mt and combined (or cpmt) snp data sets of 25 avena samples using beast v2.0.3, mrbay 3.2.6, […]

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

[…] 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 […]

PMCID: 5792620
PMID: 29435226
DOI: 10.1002/ece3.3699

[…] as well as percentage of missing data between historical and modern samples using a mann–whitney u test. finally, we generated input files for further analyses from the final vcf snps matrix using pgdspider v2.0.9.0 (lischer & excoffier, )., because (most but) not all sequences nonhomologous to the probes are filtered out during the enrichment step of hyrad, it becomes possible to retrieve […]

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, ) […]


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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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