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pgdspider [2014/07/02 12:04] – heidipgdspider [2016/02/22 15:39] (current) – heidi
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 \\ \\
-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.
  
 \\ \\
 +
  
  
 ===== Input (read) formats ===== ===== Input (read) formats =====
-  * [[PGD]]: //Version 1.0// +  * [[PGD]]: //Version 1.1// 
-  * [[Arlequin]]: //V +  * [[Arlequin]]: //Version 3.5 (24. February 2010)//
- +
- +
- +
- +
-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 61: Line 57:
   * [[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]]
Line 121: Line 120:
   * [[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.1404295451.txt.gz · Last modified: 2014/07/02 12:04 by heidi