PGDSpider version 2.0.6.0 (Juli 2014)
PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances). Besides the conventional population genetics formats, PGDSpider integrates population genomics data formats commonly used to store and handle next-generation sequencing (NGS) data. Currently, PGDSpider is not meant to convert very large NGS files as it loads into memory the whole input file, whose size may exceed available RAM. However, since PGDSpider allows one to convert specific subsets of these NGS files into any other format, one could use this feature to calculate parameters or statistics for specific regions, and thus perform sliding window analysis over large genomic regions.
PGDSpider uses a newly developed PGD (Population Genetics Data) format as an intermediate step in the conversion process. PGD is a file format designed to store various kinds of population genetics data, including different data types (e.g. DNA sequences, microsatellites, AFLP or SNPs) and ploidy levels. PGD is based on the XML format and is therefore independent of any particular computer system and extensible for future needs. PGDSpider uses PGD to connect population genetics and genomics programs like a spider knits a web.
PGDSpider is written in Java and is therefore platform independent. It is user friendly due to its intuitive graphical user interface. PGDSpider allows the user to store his preferred conversion settings for repeated conversions of similar input formats. A command line version of PGDSpider is also provided, making it possible to embed PGDSpider in data analysis pipelines.
System requirements:
PGDSpider is written in Java and therefore platform independent, but SUN Java 1.6 RE (or a newer version) has to be installed.
Copyright © 2007-2014, Heidi E.L. Lischer. All rights reserved.
PGDSpider is distributed under the BSD 3-Clause License. For the full text of the license, see the file LICENSE.txt
By using, modifying or distributing this software you agree to be bound by the terms of this license.
GenBank | gi|gi-number|gb|accession|locus |
EMBL Data Library | gi|gi-number|emb|accession|locus |
DDBJ, DNA Database of Japan | gi|gi-number|dbj|accession|locus |
General database identifier | gnl|database|identifier |
“simply” | identifier |
handled data types | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
format | extension | NGS | DNA | RNA | Microsat | SNP | RFLP | AFLP | Standard | Allele frequency | distance |
Arlequin | .arp | x | x | x | x | x | x | x | |||
BAM | .bam | x | x | x | |||||||
BAPS | .txt | x | x | x | x | x | |||||
BATWING | .txt | x | x | ||||||||
BCF | .bcf | x | x | x | x | ||||||
CONVERT | .txt | x | x | x | x | x | |||||
FASTA | no standard file extension, .fa, .mpfa, .fna, .fsa, .fas, .fasta or .txt | x | x | x | |||||||
FASTQ | no standard file extension, .fastq, .fq or .txt | x | |||||||||
FDist2 (datacal) | no standard file extension | x | x | x | x | x | x | x | |||
FSTAT | .dat | x | x | x | x | ||||||
GDA | .nex | x | x | x | x | x | |||||
GENELAND | .txt | x | x | x | x | x | |||||
GENEPOP | .txt | x | x | x | x | ||||||
GENETIX | .gtx | x | x | x | x | x | |||||
GESTE / BayeScan | no standard file extension | x | x | x | x | ||||||
HGDP-CEPH | .arp | (x) | (x) | x | (x) | (x) | (x) | ||||
Immanc | .inp or .txt | x | x | x | x | x | |||||
IM (IMa) | .u or .txt | x | x | ||||||||
IMa2 | .u or .txt | x | x | ||||||||
KML | .kml | ||||||||||
MEGA | .meg | x | x | x | |||||||
MIGRATE | no standard file extension, .txt | x | x | x | x | x | |||||
MSA | .dat, .txt | x | |||||||||
MSVar | no standard file extension | x | |||||||||
NewHybrids | .dat, .txt | x | x | x | x | ||||||
NEXUS | .nex | x | x | ||||||||
PED | .ped | x | |||||||||
PGD | .xml | x | x | x | x | x | x | x | x | x | |
PHYLIP | .txt | x | x | x | |||||||
SAM | .sam | x | x | x | |||||||
STRUCTURE | no standard file extension | x | x | x | x | x | |||||
VCF | .vcf | x | x | x | x |