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pgdspider [2014/07/02 12:05] – heidipgdspider [2014/07/02 12:15] – heidi
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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  +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.
- +
- +
- +
-to be installed.+
 \\ \\
  
Line 53: Line 49:
  
 ===== Input (read) formats ===== ===== Input (read) formats =====
-  * [[PGD]]: //Version 1 +  * [[PGD]]: //Version 1.0// 
- +  * [[Arlequin]]: //Version 3.5 (24. February 2010)//
-0 +
- +
-/ +
-  * [[Arlequin]]: //V +
- +
- +
- +
- +
-sion 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)//
Line 69: Line 56:
   * [[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:
  
Line 83: Line 71:
   * [[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)//
Line 91: Line 80:
   * [[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)\\
- +
-\\+
  
  
Line 108: Line 96:
   * [[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]]
Line 129: Line 119:
   * [[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.txt · Last modified: 2016/02/22 15:39 by heidi