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pgdspider [2013/09/19 14:48] – heidipgdspider [2016/02/22 15:39] (current) – heidi
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 ====== PGDSpider ====== ====== PGDSpider ======
 {{splashscreen.png|}}\\ {{splashscreen.png|}}\\
-**PGDSpider version 2.0.1.6 (May 2012)**+**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 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.  \\
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 ===== download PGDSpider ===== ===== download PGDSpider =====
-**[[http://www.cmpg.unibe.ch/software/PGDSpider|PGDSpider]]**+**[[http://cmpgapache.unibe.ch/cmpg-software/PGDSpider/index.htm|PGDSpider]]**
  
 [[PGD Spider - manual|PGDSpider - manual]] [[PGD Spider - manual|PGDSpider - manual]]
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 **System requirements:**\\ **System requirements:**\\
 PGDSpider is written in Java and therefore platform independent, but [[http://www.oracle.com/technetwork/java/javase/downloads/index.html|SUN Java 1.6 RE]] (or a newer version) has to be installed. PGDSpider is written in Java and therefore platform independent, but [[http://www.oracle.com/technetwork/java/javase/downloads/index.html|SUN Java 1.6 RE]] (or a newer version) has to be installed.
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 ===== How to cite PGDSpider and License ===== ===== How to cite PGDSpider and License =====
-[[http://http://bioinformatics.oxfordjournals.org/content/28/2/298|Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298-299. ]]+[[http://http://bioinformatics.oxfordjournals.org/content/28/2/298|Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298-299.]]
  
 \\ \\
-Copyright © 2007-2012, Heidi E.L. Lischer. All rights reserved.\\+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\\ 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. By using, modifying or distributing this software you agree to be bound by the terms of this license.
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-===== Input (read) formats ===== 
-  * [[PGD]]: //Version 1.0// 
-  * [[Arlequin]]: //Ve 
  
-sion 3.5 (24. February 2010)//+===== Input (read) formats ===== 
 +  * [[PGD]]: //Version 1.1// 
 +  * [[Arlequin]]: //Version 3.5 (24. February 2010)//
   * [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]]: //(17. April 2011)//   * [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]]: //(17. April 2011)//
   * [[BAPS]]: //Version 5.4 (29. April 2010)//   * [[BAPS]]: //Version 5.4 (29. April 2010)//
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   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]]: //(14. May 2011)//   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]]: //(14. May 2011)//
   * [[CONVERT]]: //Version 1.31 (March 2005)//   * [[CONVERT]]: //Version 1.31 (March 2005)//
 +  * [[Eigensoft]] (EIGENSTRAT, ANCESTRYMAP): //Version 5.0.2 (April 2014)//
   * [[FASTA]]: but only these types:   * [[FASTA]]: but only these types:
  
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   * [[GENEPOP]]: //Version 4.1 (24. March 2011)//   * [[GENEPOP]]: //Version 4.1 (24. March 2011)//
   * [[GENETIX]]: //Version 4.05 (5. May 2004)//   * [[GENETIX]]: //Version 4.05 (5. May 2004)//
 +  * [[HGDP]]: //Stanford//
   * [[HGDP-CEPH]] (Arlequin + log file): //Version 3.0//   * [[HGDP-CEPH]] (Arlequin + log file): //Version 3.0//
   * [[Immanc]] (BayesAss): //Version 5.0 (8. October 1998)//   * [[Immanc]] (BayesAss): //Version 5.0 (8. October 1998)//
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   * [[MSA]]: //Version 4.05//   * [[MSA]]: //Version 4.05//
   * [[NewHybrids]]: //Version 1.1 beta (7. April 2003)//   * [[NewHybrids]]: //Version 1.1 beta (7. April 2003)//
-  * [[NEXUS]] (DNA/ RNA/ NUCLEOTIDE)+  * [[NEXUS]] 
 +  * [[ONeSAMP]]: //Version 1.2//
   * [[PED]]   * [[PED]]
   * [[PHYLIP]] (DNA/ RNA /distance matrix): //Version 3.69 (September 2009)//   * [[PHYLIP]] (DNA/ RNA /distance matrix): //Version 3.69 (September 2009)//
   * [[http://phd.chnebu.ch/index.php/SAMtools|SAM]]: //Version 1.4 (17. April 2011)//   * [[http://phd.chnebu.ch/index.php/SAMtools|SAM]]: //Version 1.4 (17. April 2011)//
   * [[STRUCTURE]]: //Version 2.3.3 (January 2010)//   * [[STRUCTURE]]: //Version 2.3.3 (January 2010)//
-  * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]: //4.1 (2. August 2012)// without structural variants (only SNP and INDELs) +  * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]: //4.1 (2. August 2012)// without structural variants (only SNP and INDELs)\\
- +
-\\+
  
  
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   * [[Arlequin]]: //Version 3.5 (24. February 2010)//   * [[Arlequin]]: //Version 3.5 (24. February 2010)//
   * [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]]: //(17. April 2011)//   * [[http://phd.chnebu.ch/index.php/SAMtools#BAM_format|BAM]]: //(17. April 2011)//
 +  * [[BAMOVA]]: //Version 1.02 (27.9.2911)//
   * [[BAPS]]: //Version 5.4 (29. April 2010)//   * [[BAPS]]: //Version 5.4 (29. April 2010)//
   * [[BATWING]]: //(2003)//   * [[BATWING]]: //(2003)//
   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]]: //(14. May 2011)//   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)#Binary_variant_Call_Format_.28BCF.29|BCF]]: //(14. May 2011)//
 +  * [[Eigensoft]] (EIGENSTRAT, ANCESTRYMAP): //Version 5.0.2 (April 2014)//
   * [[FASTA]]   * [[FASTA]]
   * [[FASTQ]]   * [[FASTQ]]
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   * [[MSVar]]: //Version 0.4.1.b (7. April 1999)//   * [[MSVar]]: //Version 0.4.1.b (7. April 1999)//
   * [[NewHybrids]]: //Version 1.1 beta (7. April 2003)//   * [[NewHybrids]]: //Version 1.1 beta (7. April 2003)//
-  * [[NEXUS]] (DNA/ RNA/ NUCLEOTIDE)+  * [[NEXUS]] 
 +  * [[ONeSAMP]]: //Version 1.2//
   * [[PED]]   * [[PED]]
   * [[PHYLIP]] (DNA/ RNA /distance matrix): //Version 3.69 (September 2009)//   * [[PHYLIP]] (DNA/ RNA /distance matrix): //Version 3.69 (September 2009)//
   * [[http://phd.chnebu.ch/index.php/SAMtools|SAM]]: //Version 1.4 (17. April 2011)//   * [[http://phd.chnebu.ch/index.php/SAMtools|SAM]]: //Version 1.4 (17. April 2011)//
 +  * [[Structurama]]
   * [[STRUCTURE]]: //Version 2.3.3 (January 2010)//   * [[STRUCTURE]]: //Version 2.3.3 (January 2010)//
   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]: //4.1 (2. August 2012)// without structural variants (only SNP and INDELs)   * [[http://phd.chnebu.ch/index.php/Variant_Call_Format_(VCF)|VCF]]: //4.1 (2. August 2012)// without structural variants (only SNP and INDELs)
pgdspider.1379594917.txt.gz · Last modified: 2013/09/19 14:48 by heidi