ANGSD: Analysis of next generation Sequencing Data
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User contributions for Albrecht
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18 July 2017
- 15:1015:10, 18 July 2017 diff hist −1 HWE test →example
- 15:0815:08, 18 July 2017 diff hist +164 HWE test →example
- 14:5114:51, 18 July 2017 diff hist +2 HWE test →Use as a filter
- 14:5014:50, 18 July 2017 diff hist +13 HWE test No edit summary
- 14:5014:50, 18 July 2017 diff hist −181 HWE test No edit summary
3 March 2017
- 12:1612:16, 3 March 2017 diff hist +170 Filters →Number of non missing individuals
- 11:5811:58, 3 March 2017 diff hist −31 Filters →Extra
- 11:5611:56, 3 March 2017 diff hist +226 Filters →Extra
24 January 2017
- 14:3914:39, 24 January 2017 diff hist −1 Filters →Selected Sites
- 14:2614:26, 24 January 2017 diff hist +151 PCA MDS →Options
- 14:2414:24, 24 January 2017 diff hist +2 PCA MDS →single read sampling approach for PCA or MDS
- 14:2314:23, 24 January 2017 diff hist +263 PCA MDS No edit summary
- 14:1814:18, 24 January 2017 diff hist +1 PCA MDS No edit summary
- 14:1714:17, 24 January 2017 diff hist +26 PCA MDS No edit summary
16 November 2016
- 18:2018:20, 16 November 2016 diff hist +199 Fasta No edit summary
- 18:1918:19, 16 November 2016 diff hist +702 Fasta →Options
- 18:1318:13, 16 November 2016 diff hist +126 Fasta →Brief Overview
14 July 2016
- 16:4616:46, 14 July 2016 diff hist +3 Relatedness →IBS/genotype distribution
- 11:1611:16, 14 July 2016 diff hist +881 Genotype Distribution →Example current
- 11:0211:02, 14 July 2016 diff hist +6,368 Genotype Distribution No edit summary
- 10:4710:47, 14 July 2016 diff hist +94 Genotype Distribution No edit summary
- 10:4310:43, 14 July 2016 diff hist +946 Genotype Distribution No edit summary
- 10:3810:38, 14 July 2016 diff hist +4,100 Genotype Distribution No edit summary
12 July 2016
- 16:2816:28, 12 July 2016 diff hist 0 N File:RatioRel.png No edit summary current
- 16:2816:28, 12 July 2016 diff hist +41 Relatedness →IBS/genotype distribution
- 16:0216:02, 12 July 2016 diff hist +141 Relatedness →IBS/genotype distribution
- 15:5815:58, 12 July 2016 diff hist +302 Relatedness →How to get the IBS pattern
- 15:5515:55, 12 July 2016 diff hist +2 Relatedness No edit summary
- 15:5515:55, 12 July 2016 diff hist +12 N Genotype Distribution Created page with "comming soon"
- 15:5315:53, 12 July 2016 diff hist +299 Relatedness →IBS/genotype distribution
- 15:4715:47, 12 July 2016 diff hist +18 Relatedness No edit summary
- 15:4615:46, 12 July 2016 diff hist +60 Relatedness →IBS/genotype distribution
- 15:4315:43, 12 July 2016 diff hist +126 Relatedness →IBS/genotype distribution
- 15:3015:30, 12 July 2016 diff hist +243 Relatedness No edit summary
- 15:2215:22, 12 July 2016 diff hist +1,185 Relatedness No edit summary
- 15:0615:06, 12 July 2016 diff hist +2 Relatedness →IBS/genotype distribution
- 15:0515:05, 12 July 2016 diff hist +271 Relatedness →IBS/genotype distribution
- 15:0215:02, 12 July 2016 diff hist +87 Relatedness →NGSrelate - estimation of IBD probabilities
- 15:0115:01, 12 July 2016 diff hist −3 Relatedness →IBS/genotype distribution
- 14:5514:55, 12 July 2016 diff hist +444 Relatedness No edit summary
- 14:5314:53, 12 July 2016 diff hist +746 Relatedness No edit summary
- 14:2514:25, 12 July 2016 diff hist +4 Relatedness No edit summary
- 14:2514:25, 12 July 2016 diff hist +4 Relatedness No edit summary
- 14:2514:25, 12 July 2016 diff hist +703 N Relatedness Created page with " * NGSrelate - estimation of kinship coefficients In order to estimate kinship coefficient then population allele frequencies are needed. These can be estimated from data if ..."
- 14:2014:20, 12 July 2016 diff hist +2 MediaWiki:Sidebar No edit summary
- 14:1914:19, 12 July 2016 diff hist +88 MediaWiki:Sidebar No edit summary
7 June 2016
- 17:3317:33, 7 June 2016 diff hist 0 PCA MDS →sampled bases *ibs.gz
31 May 2016
- 14:3114:31, 31 May 2016 diff hist +30 PCA MDS No edit summary
- 13:4713:47, 31 May 2016 diff hist 0 PCA MDS No edit summary
- 13:4613:46, 31 May 2016 diff hist +222 PCA MDS →MDS/PCA using R
16 May 2016
- 13:2113:21, 16 May 2016 diff hist +8 PCA MDS →IBS
- 13:2013:20, 16 May 2016 diff hist +90 PCA MDS →Covariance
- 12:0712:07, 16 May 2016 diff hist 0 PCA MDS →Options
13 May 2016
- 13:3613:36, 13 May 2016 diff hist +188 PCA No edit summary
11 May 2016
- 10:3210:32, 11 May 2016 diff hist −95 PCA MDS →samples base *.ibsMat
28 April 2016
- 11:1611:16, 28 April 2016 diff hist +93 Genotype Likelihoods →SYK (Kim et al.)
- 11:1311:13, 28 April 2016 diff hist +11 Genotype Likelihoods →SYK (Kim et al.)
27 April 2016
- 18:5318:53, 27 April 2016 diff hist +2 PCA MDS →Output
- 18:5218:52, 27 April 2016 diff hist +6 PCA MDS →MDS/PCA using R
- 18:5118:51, 27 April 2016 diff hist 0 N File:PCA MDS.png No edit summary current
- 18:5118:51, 27 April 2016 diff hist 0 PCA MDS →MDS/PCA using R
- 18:4918:49, 27 April 2016 diff hist 0 File:IBD PCA.pdf Albrecht uploaded a new version of "File:IBD PCA.pdf" current
- 17:0717:07, 27 April 2016 diff hist +4 PCA MDS →MDS/PCA using R
- 17:0717:07, 27 April 2016 diff hist 0 N File:IBD PCA.pdf No edit summary
- 17:0617:06, 27 April 2016 diff hist +18 PCA MDS →MDS/PCA using R
- 17:0317:03, 27 April 2016 diff hist +406 PCA MDS No edit summary
- 17:0117:01, 27 April 2016 diff hist +54 PCA MDS →Model
- 16:4816:48, 27 April 2016 diff hist +1,455 PCA MDS →Output
- 16:4516:45, 27 April 2016 diff hist −160 PCA MDS →samples base *ibsMat
- 16:4416:44, 27 April 2016 diff hist +1,454 PCA MDS →Output
- 16:4316:43, 27 April 2016 diff hist +96 PCA MDS →Output
- 16:4216:42, 27 April 2016 diff hist −272 PCA MDS →Output
- 16:4116:41, 27 April 2016 diff hist +2,921 PCA MDS →Output
- 16:3416:34, 27 April 2016 diff hist −87 PCA MDS No edit summary
- 16:3316:33, 27 April 2016 diff hist +18 PCA MDS →Options
- 16:3216:32, 27 April 2016 diff hist +175 PCA MDS →Options
- 12:4712:47, 27 April 2016 diff hist +4,143 PCA MDS →single read sampling approach for PCA or MDS
- 12:2412:24, 27 April 2016 diff hist +143 PCA MDS No edit summary
- 12:2312:23, 27 April 2016 diff hist 0 PCA No edit summary
- 12:2212:22, 27 April 2016 diff hist +632 PCA No edit summary
- 12:2212:22, 27 April 2016 diff hist +48 N PCA MDS Created page with "= single read sampling approach for PCA or MDS ="
- 12:1212:12, 27 April 2016 diff hist +62 MediaWiki:Sidebar No edit summary
10 April 2016
- 18:0218:02, 10 April 2016 diff hist +8 HWE test No edit summary
- 17:5917:59, 10 April 2016 diff hist +207 HWE test No edit summary
- 17:4817:48, 10 April 2016 diff hist +2 HWE and Inbreeding estimates →Site estimate of inbreeding coefficient (HWE test)
- 17:2617:26, 10 April 2016 diff hist +5 HWE test No edit summary
- 17:2617:26, 10 April 2016 diff hist +184 HWE test →Use as a filter
- 17:1617:16, 10 April 2016 diff hist +567 HWE test No edit summary
- 17:0617:06, 10 April 2016 diff hist 0 HWE and Inbreeding estimates →Site estimate of inbreeding coefficient (HWE test)
- 17:0517:05, 10 April 2016 diff hist 0 HWE test →Output
- 17:0417:04, 10 April 2016 diff hist +7 HWE test →Output
- 17:0417:04, 10 April 2016 diff hist +439 HWE test →Output
- 17:0017:00, 10 April 2016 diff hist +1,847 N HWE test Created page with "Test for Hardy Weinberg equilibrium based on genotype likelihoods. This class works both as a filter for all other classes and outputs the results in a file. If you want to ..."
- 16:4516:45, 10 April 2016 diff hist +32 MediaWiki:Sidebar No edit summary
14 March 2016
- 10:3310:33, 14 March 2016 diff hist 0 Haploid calling →Output
- 10:3310:33, 14 March 2016 diff hist +168 Haploid calling →Output
13 March 2016
- 13:3413:34, 13 March 2016 diff hist +2 Haploid calling No edit summary
- 13:3313:33, 13 March 2016 diff hist 0 Haploid calling No edit summary
11 March 2016
- 11:4611:46, 11 March 2016 diff hist +2,758 Abbababa No edit summary current
8 March 2016
- 12:1212:12, 8 March 2016 diff hist −71 Association →Case control association using allele frequencies
15 February 2016
- 11:2111:21, 15 February 2016 diff hist +81 Abbababa No edit summary
8 February 2016
- 17:2417:24, 8 February 2016 diff hist +125 Fasta →EBD
- 17:1917:19, 8 February 2016 diff hist −2 Fasta →EBD
- 17:1917:19, 8 February 2016 diff hist −143 Fasta No edit summary
- 17:1817:18, 8 February 2016 diff hist +3 Fasta No edit summary
- 17:1717:17, 8 February 2016 diff hist +2 Fasta →Brief Overview
- 17:1517:15, 8 February 2016 diff hist +131 Fasta →Brief Overview
- 16:4016:40, 8 February 2016 diff hist +246 Fasta →Options
28 January 2016
- 11:1711:17, 28 January 2016 diff hist +115 Haploid calling No edit summary
22 January 2016
- 14:3514:35, 22 January 2016 diff hist +3 Abbababa →Options
- 14:3514:35, 22 January 2016 diff hist +346 Abbababa No edit summary
- 12:0112:01, 22 January 2016 diff hist +54 Abbababa →Example
- 11:4711:47, 22 January 2016 diff hist +27 Plink →NB
- 11:4611:46, 22 January 2016 diff hist −1 Plink →Example
- 11:4411:44, 22 January 2016 diff hist +10 Genotype calling →Example
3 January 2016
- 19:2419:24, 3 January 2016 diff hist +3 MediaWiki:Sidebar No edit summary
- 19:2119:21, 3 January 2016 diff hist +6 MediaWiki:Sidebar No edit summary
- 16:2816:28, 3 January 2016 diff hist −32 Haploid calling →Output
- 16:2716:27, 3 January 2016 diff hist +2,256 N Haploid calling Created page with "Simple haploid output based on sampling or consensus. __TOC__ <classdiagram type="dir:LR"> [BAM files{bg:orange}]->[Sequence data|Random base;Consensus base] [sequence da..."
- 16:1516:15, 3 January 2016 diff hist +35 MediaWiki:Sidebar No edit summary
16 December 2015
- 17:3017:30, 16 December 2015 diff hist +59 MsToGlf No edit summary
4 December 2015
- 17:1117:11, 4 December 2015 diff hist −1 Filters →Extra
- 17:1117:11, 4 December 2015 diff hist −98 Filters →Extra
- 16:2316:23, 4 December 2015 diff hist +18 Input →Genotype Probability Files
- 16:2216:22, 4 December 2015 diff hist 0 Input →Tutorial
- 16:2216:22, 4 December 2015 diff hist +1,823 Input →-glf
- 16:1816:18, 4 December 2015 diff hist +790 Supersim No edit summary current
- 15:5515:55, 4 December 2015 diff hist −1 Input →Arguments
- 15:5515:55, 4 December 2015 diff hist 0 Input →Example
- 15:5415:54, 4 December 2015 diff hist 0 Input →Example
- 15:5415:54, 4 December 2015 diff hist 0 Input →Tutorial
- 15:5315:53, 4 December 2015 diff hist +4,725 Input →Genotype Probability Files
- 15:5215:52, 4 December 2015 diff hist −488 Input →VCF files
- 15:4615:46, 4 December 2015 diff hist +4,114 Input →VCF files
- 15:1715:17, 4 December 2015 diff hist −161 Input →Genotype Probability Files
- 15:1615:16, 4 December 2015 diff hist +29 Input No edit summary
- 15:1315:13, 4 December 2015 diff hist +788 Input →Genotype Probability Files
- 14:5614:56, 4 December 2015 diff hist +51 Input →Pileup files
- 14:5214:52, 4 December 2015 diff hist −5 Input →Tutorial
- 14:3314:33, 4 December 2015 diff hist +43 Input →Genotype Probability Files
- 14:2314:23, 4 December 2015 diff hist −12 Input No edit summary
- 14:2114:21, 4 December 2015 diff hist +11 Input No edit summary
- 14:1914:19, 4 December 2015 diff hist +62 Input →Pileup files
- 13:3113:31, 4 December 2015 diff hist +2,787 Input →Pileup files
- 12:0512:05, 4 December 2015 diff hist +14 Input →BAM/CRAM
- 12:0112:01, 4 December 2015 diff hist 0 Input No edit summary
- 12:0112:01, 4 December 2015 diff hist +535 Input →BAM/CRAM
- 11:4811:48, 4 December 2015 diff hist +17 Input →Sequence data (BAM/CRAM/mpileup)
- 11:3711:37, 4 December 2015 diff hist +48 Input →BAM/CRAM
- 11:3711:37, 4 December 2015 diff hist +120 Input →Sequence data (BAM/CRAM/mpileup)
- 11:2811:28, 4 December 2015 diff hist −100 Input No edit summary
- 11:2711:27, 4 December 2015 diff hist +234 Input No edit summary
- 11:2211:22, 4 December 2015 diff hist +12 Input No edit summary
- 11:2011:20, 4 December 2015 diff hist −367 Quick Start No edit summary
- 11:1911:19, 4 December 2015 diff hist −161 Quick Start →Examples
- 10:5610:56, 4 December 2015 diff hist +12 Quick Start →Ancestral fasta file for hg19
- 10:5210:52, 4 December 2015 diff hist +33 Quick Start No edit summary
- 10:4910:49, 4 December 2015 diff hist −92 MediaWiki:Sitenotice No edit summary
19 November 2015
- 17:1317:13, 19 November 2015 diff hist +35 MediaWiki:Sidebar No edit summary
12 November 2015
- 20:1920:19, 12 November 2015 diff hist +103 MsToGlf No edit summary
11 July 2015
- 15:5115:51, 11 July 2015 diff hist +811 Contamination No edit summary current
28 June 2015
- 14:0114:01, 28 June 2015 diff hist +1 Plink No edit summary
5 April 2015
- 19:5219:52, 5 April 2015 diff hist +318 Genotype calling →options
15 December 2014
- 19:5019:50, 15 December 2014 diff hist −8 SYKmaf Undo revision 2344 by Albrecht (talk) current
- 19:4919:49, 15 December 2014 diff hist +8 SYKmaf →ML estimator with unknown minor
25 August 2014
- 13:5813:58, 25 August 2014 diff hist −566 Association →Output
- 13:5613:56, 25 August 2014 diff hist +228 Association →Score statistic
- 13:4913:49, 25 August 2014 diff hist +201 Change log →Latest
27 June 2014
- 14:3514:35, 27 June 2014 diff hist −1,005 Contamination →method
- 14:3514:35, 27 June 2014 diff hist +1,005 N Rasmussen2011 Created page with "[http://www.ncbi.nlm.nih.gov/entrez?Db=pubmed&Cmd=ShowDetailView&uid=21940856 PMID 21940856], [http://www.bioinformatics.org/texmed/cgi-bin/list.cgi?PMID=21940856 bibtex ] Ras..." current
- 14:3414:34, 27 June 2014 diff hist +59 Citing angsd No edit summary
- 14:3214:32, 27 June 2014 diff hist +174 Orlando2013 No edit summary current
- 14:2914:29, 27 June 2014 diff hist +1,084 Contamination No edit summary
- 14:0614:06, 27 June 2014 diff hist +35 Contamination No edit summary
- 13:5913:59, 27 June 2014 diff hist +401 Contamination →Output
26 June 2014
- 13:2213:22, 26 June 2014 diff hist +14 Thetas,Tajima,Neutrality tests →Example
- 13:1813:18, 26 June 2014 diff hist −65 Thetas,Tajima,Neutrality tests →Example
- 13:1613:16, 26 June 2014 diff hist +203 Thetas,Tajima,Neutrality tests →Example
- 12:4512:45, 26 June 2014 diff hist +131 Major Minor No edit summary
- 12:4212:42, 26 June 2014 diff hist +53 Major Minor →Pre specified Major using a reference
- 12:4112:41, 26 June 2014 diff hist −1 Major Minor →Pre specified Major using a reference
- 12:3412:34, 26 June 2014 diff hist −34 User:Albrecht Blanked the page current
24 June 2014
- 12:4612:46, 24 June 2014 diff hist +3 Input →Brief Overview
13 May 2014
- 17:1517:15, 13 May 2014 diff hist +556 Genotype Likelihoods →Output
23 April 2014
- 16:1916:19, 23 April 2014 diff hist +190 Major Minor No edit summary
- 16:1616:16, 23 April 2014 diff hist −111 MediaWiki:Sitenotice No edit summary
- 16:1516:15, 23 April 2014 diff hist +12 ANGSD No edit summary
6 March 2014
- 13:2613:26, 6 March 2014 diff hist −8 SFS Estimation →How to plot
- 13:2513:25, 6 March 2014 diff hist −6 SFS Estimation →How to plot
- 13:2513:25, 6 March 2014 diff hist −19 SFS Estimation →Format specification of binary .saf file
- 13:2113:21, 6 March 2014 diff hist −56 SFS Estimation →Folded spectra
- 13:1613:16, 6 March 2014 diff hist +49 SFS Estimation →Interpretation of the emOptim2 output file
- 13:1513:15, 6 March 2014 diff hist +347 SFS Estimation →Options
- 12:2712:27, 6 March 2014 diff hist +148 SFS Estimation →Options
- 12:2612:26, 6 March 2014 diff hist +52 SFS Estimation →Posterior per-site distributions of the sample allele frequency
- 12:2312:23, 6 March 2014 diff hist +13 SFS Estimation →Interpretation of output file
- 12:2312:23, 6 March 2014 diff hist +47 SFS Estimation →Interpretation of output file
- 12:2012:20, 6 March 2014 diff hist −3 SFS Estimation →Example
- 12:2012:20, 6 March 2014 diff hist +155 SFS Estimation →Example
- 12:1812:18, 6 March 2014 diff hist +188 SFS Estimation →Brief Overview
- 12:1712:17, 6 March 2014 diff hist −64 SFS Estimation →Example
- 12:1612:16, 6 March 2014 diff hist +98 SFS Estimation →Example
- 12:1512:15, 6 March 2014 diff hist −1 SFS Estimation →Example
- 12:1112:11, 6 March 2014 diff hist +1 SFS Estimation →How to plot
- 12:1012:10, 6 March 2014 diff hist +43 SFS Estimation →How to plot
- 12:0912:09, 6 March 2014 diff hist −2,070 SFS Estimation →Theory
- 12:0912:09, 6 March 2014 diff hist −11 RealSFSmethod →Theory
- 12:0812:08, 6 March 2014 diff hist +2,068 N RealSFSmethod Created page with "=Theory= <pre> We will try to elaborate on the theory behind the methods. Below is only a preliminary version of the theory. </pre> This method is described in Nielsen2012..."
- 12:0812:08, 6 March 2014 diff hist +6 SFS Estimation No edit summary
- 12:0812:08, 6 March 2014 diff hist +2 SFS Estimation No edit summary
- 12:0812:08, 6 March 2014 diff hist +64 SFS Estimation No edit summary
- 12:0612:06, 6 March 2014 diff hist +161 SFS Estimation →Options
- 12:0312:03, 6 March 2014 diff hist +67 SFS Estimation No edit summary
- 11:5311:53, 6 March 2014 diff hist −9 Thetas,Tajima,Neutrality tests →Example
- 11:5211:52, 6 March 2014 diff hist −9 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5211:52, 6 March 2014 diff hist +4 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5111:51, 6 March 2014 diff hist +4 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:5011:50, 6 March 2014 diff hist −4 Thetas,Tajima,Neutrality tests →Example
- 11:5011:50, 6 March 2014 diff hist +16 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4611:46, 6 March 2014 diff hist +26 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4411:44, 6 March 2014 diff hist +170 Thetas,Tajima,Neutrality tests →Unknown ancestral state (folded sfs)
- 11:4011:40, 6 March 2014 diff hist +33 Thetas,Tajima,Neutrality tests →Sliding Window example
- 11:3811:38, 6 March 2014 diff hist +129 Thetas,Tajima,Neutrality tests →.thetas.gz is
- 11:3711:37, 6 March 2014 diff hist +67 Thetas,Tajima,Neutrality tests →Example
- 11:3611:36, 6 March 2014 diff hist −18 Thetas,Tajima,Neutrality tests →Sliding Window example
- 11:2711:27, 6 March 2014 diff hist +1 Thetas,Tajima,Neutrality tests →Example
- 11:2511:25, 6 March 2014 diff hist +72 Thetas,Tajima,Neutrality tests →Example
- 11:0911:09, 6 March 2014 diff hist +39 Thetas,Tajima,Neutrality tests →Example
5 March 2014
- 20:1520:15, 5 March 2014 diff hist +1 Filters →Extra
- 20:1420:14, 5 March 2014 diff hist +16 Plink →Example
- 20:1220:12, 5 March 2014 diff hist −11 Filters →Extra
- 20:1220:12, 5 March 2014 diff hist −2 Plink →Example
- 20:0920:09, 5 March 2014 diff hist 0 Plink No edit summary
- 20:0820:08, 5 March 2014 diff hist 0 Plink →Example
- 20:0120:01, 5 March 2014 diff hist −5 Plink No edit summary
- 20:0020:00, 5 March 2014 diff hist +38 MediaWiki:Sidebar No edit summary
- 19:3819:38, 5 March 2014 diff hist +29 Association →Example with imputation (using BEAGLE)
- 19:3619:36, 5 March 2014 diff hist +556 Association →Example with imputation (using BEAGLE)
- 19:3519:35, 5 March 2014 diff hist +279 Input →Genotype Probability Files
- 19:1819:18, 5 March 2014 diff hist −998 Bugs No edit summary
- 19:1019:10, 5 March 2014 diff hist +418 Association →Example
- 19:0619:06, 5 March 2014 diff hist −39 MediaWiki:Sidebar No edit summary
- 19:0519:05, 5 March 2014 diff hist +405 Beagle input →output
- 18:5918:59, 5 March 2014 diff hist −29 Beagle input →Example
- 18:5818:58, 5 March 2014 diff hist +139 Beagle input No edit summary
- 18:5418:54, 5 March 2014 diff hist −45 SNP calling No edit summary
26 February 2014
- 20:0420:04, 26 February 2014 diff hist +11 SNP calling No edit summary
- 18:4318:43, 26 February 2014 diff hist −43 Allele Frequencies →.mafs
- 18:4318:43, 26 February 2014 diff hist −1 Allele Frequencies →.mafs
- 18:4318:43, 26 February 2014 diff hist +8 Allele Frequencies →.mafs