PGDSpider pipeline

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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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 citation

2016
PMCID: 5087884

[…] populations based on sample location (fig 1, table 1). genotypes were output in vcf format for downstream filtering and analysis., all filtering of snp loci was carried out using vcftools v. 1.12b. pgdspider (v. 2.0.5.2) [42] was used to convert vcf files to all other formats, including genepop [43], structure [44, 45] and arlequin [46]. first, rad-tags containing more than three snps per tag […]

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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