PGDSpider version 2.1.1.5 (May 2018)
An automated data conversion tool for connecting population genetics and genomics programs
Download and Installation Instructions
Formats supported by PGDSpider
How to cite PGDSpider and License
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.
PGDSpider is written in Java and therefore platform independent, but SUN Java 1.7 RE (or a newer version. At the moment it will not run under Java 9!) has to be installed. Java 8 RE can be downloaded under following link:
http://www.oracle.com/technetwork/java/javase/downloads/index.html
Download and Installation Instructions
Install the Java7 RE (or a newer version. At the moment it will not run under Java 9!)
Windows:
download and install Java RE with following link:
http://www.oracle.com/technetwork/java/javase/downloads/index.html
Linux:
Ubuntu/Debian:
Execute the following command as a root user:
"apt-get install openjdk-7-jre"
Other LINUX distributions:
http://www.oracle.com/technetwork/java/javase/downloads/index.html
Mac:
Apple Computer supplies their own version of Java. Use the
Software Update
feature (available on the Apple menu) to check that you have the most up-to-date version of Java for your Mac.
If you have problems with downloading, installing or using Java on Mac, please contact Apple Computer Technical Support.
2nd step:
Download the PGDSpider application and unzip it on the local drive: PGDSpider (2.1.1.5) - Download
PGDSpider user manual: PGDSpider manual_vers 2-1-1-5.pdf
changes: changelog.txt
simple example files to do some trial format conversion with PGDSpider: examples.zip
Execute PGDSpider GUI:
Windows:
execute the file
"PGDSpider2.exe"
to start the program
Linux:
execute the command
"./PGDSpider2.sh"
to start the program
Mac and others:
execute the command
"java -Xmx1024m -Xms512m -jar PGDSpider2.jar"
to start the program
Execute PGDSpider-cli (command line):
Windows:
execute the command
"PGDSpider2-cli.exe"
Linux:
execute the command
"java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar"
Mac and others:
execute the command
"java -Xmx1024m -Xms512m -jar PGDSpider2-cli.jar"
Java Web Start:
Additionally we provide the possibility to download and run PGDSpider from the web by the Java
Web Start software. Java Web Start provides an easy, one-click activation of PGDSpider and it
guarantees that you are always running the latest version.
Java Web Start is included in the Java Runtime Environment. Have a look at
Installation Instructions under
1st step
to get information on how to get Java6 RE (or a newer version).
Launch PGDSpider using Java Web Start:
Limitations: Starting PGDSpider from Java Web Start it is not possible to change the amount of memory PGDSpider is allowed to use (by default it is set to 1 GB).
Formats supported by PGDSpider:
PGDSpider is able to parse 33 and to write 36 different file formats:
Data format | Version | References and Links | External dependency | Input format | Output format |
PGD | 1.1 | Lischer and Excoffier, 2012 | x | x | |
Arlequin |
3.5 (12.4.2015) |
Excoffier and Lischer, 2010 | x | x | |
BAM | (17.4.2011) | Li et al., 2009 | SAMtools, BCFtools | x | x |
BAMOVA |
1.02 (27.9.2011) |
Gompert and Buerkle, 2011; Gompert et al., 2010 | x | ||
BAPS |
6.0 (17.12.2012) |
Tang et al., 2009 | x | x | |
BATWING | (2003) | Wilson et al., 2003 | x | x | |
Bayenv |
2.0 (20.11.2013) |
Coop et al., 2010; Gunther and Coop, 2013 | x | ||
BCF | (14.5.2011) | SAMtools, BCFtools | x | x | |
CONVERT |
1.31 (March 2005) |
Glaubitz, 2004 | x | ||
EIGENSOFT |
5.0.2 (April 2014) |
Patterson et al., 2006; Price et al., 2006 | x | x | |
extended multi-FASTA (XMFA) | x | x | |||
FASTA | Pearson, 1990 | x | x | ||
FASTQ | Cock, et al., 2010 | x | x | ||
FDist2 (datacal) | Beaumont and Nichols, 1996; Flint et al., 1999 | x | |||
FSTAT |
2.9.3.2 (February 2002) |
Goudet, 2001 | x | x | |
GDA |
1.1 (7.1.2002) |
Lewis, 2001 | x | x | |
GENELAND | (12.04.2011) |
Guillot, 2008; Guillot et al., 2005; Guillot and Santos, 2009;
Guillot and Santos, 2010; Guillot et al.,2008 |
x | x | |
GENEPOP |
4.1 (24.03.2011) |
Rousset, 2008 | x | x | |
GENETIX |
4.05 (5.5.2004) |
Belkhir, 1996-2004 | x | x | |
GESTE /
BayeScan |
GESTE: 2.0 BayeScan 2.01 (December 2010) |
GESTE: Foll and Gaggiotti, 2006
BayeScan: Fischer et al., 2011; Foll et al., 2010; Foll and Gaggiotti, 2008 |
x | ||
HGDP | Stanford | x | |||
HGDP-CEPH
(Arlequin + log file) |
3.0 | x | |||
Immanc (BayesAss) |
5.0 (8.10.1998) |
Rannala, Mountain, 1997; Wilson, Rannala, 2003 | x | x | |
IM (IMa) | (17.12.2009) | Hey and Nielsen, 2004, 2007; Nielsen and Wakeley, 2001 | x | x | |
IMa2 | (26.08.2011) | Hey, 2010 | x | x | |
KML | 2.2 | Google 2009 | x | ||
MAF | 1 | x | |||
MEGA |
5 (24.4.2011) |
Tamura et al., 2011 | x | x | |
MIGRATE |
3.2.6 (13.10.2010) |
Beerli, 2009 | x | x | |
MSA | 4.05 | Dieringer, Schlotterer, 2003 | x | x | |
MSVar |
0.4.1.b (7.4.1999) |
Beaumont, 1999 | x | ||
NewHybrids |
1.1 beta (7.4.2003) |
Anderson and Thompson, 2002 | x | x | |
NEXUS |
Maddison et al., 1997
--> able to read CharSet definitions within a MrBayes block |
x | x | ||
ONeSAMP | 1.2 | Tallmon et al., 2008 | x | x | |
PED | Purcell et al., 2007 | x | x | ||
PHYLIP (RAxML) |
3.69 (September 2009) |
Felsenstein, 1989; Felsenstein, 2004 | x | x | |
SAM |
1.4 (17.4.2011) |
Li et al. 2009 | SAMtools, BCFtools | x | x |
Structurama | Huelsenbeck et al., 2011 | x | |||
STRUCTURE (fastSTRUCTURE) |
2.3.4 (July 2012) |
Falush et al., 2003; Falush et al., 2007; Pritchard et al., 2000; Hubisz et al., 2009; Raj et al., 2014 |
x | x | |
VCF |
4.1 (2.8.2012) |
--> without structural variants (only SNP and INDELs) | SAMtools, BCFtools | x | x |
Note that, PGDSpider is currently not meant to convert large NGS files as it loads into memory the whole input file,
which may lead to memory issues. However, PGDSpider allows one to convert specific subsets of these NGS files into
any other format, and this approach can be used to perform sliding windows analyses on large NGS files.
Help
If you have any problems:
read the user manual:
PGDSpider manual_vers 2-1-1-5.pdf
read the help file which can be found in the "Config" menu of the PGDSpider
Screenshot
PGDSpider GUI:
SPID Editor:
How to cite PGDSpide and License
Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298-299.
Copyright (c) 2007-2018, 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.
If there are any bugs, send me an e-mail. Please give me a short description of the bug and tell me the input and output file format.
If it is possible also attach the input file which caused the problem.
PGDSpider is an on-going project. For any comments or suggestions of further file formats, please send me an e-mail.
e-mail: heidi.lischer(at)iee.unibe.ch
Heidi Lischer
and Laurent Excoffier
Computational and Molecular Population Genetics lab (CMPG)
Institute of Ecology and Evolution (IEE)
University of Berne
3012 Bern
Switzerland
members of the Swiss Institute of Bioinformatics (SIB)
07.05.2018