ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
User contributions for Thorfinn
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30 June 2014
- 13:1113:11, 30 June 2014 diff hist −16 Quick Start →Ancestral fasta file for hg19
- 13:0113:01, 30 June 2014 diff hist −2 Thetas,Tajima,Neutrality tests →Step 2: Calculate the thetas for each site
- 13:0013:00, 30 June 2014 diff hist −2 Thetas,Tajima,Neutrality tests →Step 1: Finding a 'global estimate' of the SFS
- 13:0013:00, 30 June 2014 diff hist +783 Thetas,Tajima,Neutrality tests →Example
- 12:5812:58, 30 June 2014 diff hist −567 Thetas,Tajima,Neutrality tests →Full command list for above examples
- 12:5812:58, 30 June 2014 diff hist +1 Thetas,Tajima,Neutrality tests →=Step 3b: Sliding Window example
- 12:5812:58, 30 June 2014 diff hist +10 Thetas,Tajima,Neutrality tests →Sliding Window example
- 12:5812:58, 30 June 2014 diff hist +1 Thetas,Tajima,Neutrality tests →Step 3: Estimate Tajimas D and other statistics
- 12:5712:57, 30 June 2014 diff hist +77 Thetas,Tajima,Neutrality tests →Full command list for above examples
- 12:5612:56, 30 June 2014 diff hist +433 Thetas,Tajima,Neutrality tests →Full command list for above examples
- 12:5412:54, 30 June 2014 diff hist +57 Thetas,Tajima,Neutrality tests →Example Output
- 12:5312:53, 30 June 2014 diff hist −6 Thetas,Tajima,Neutrality tests →Output of the .thetas.gz file
- 12:5312:53, 30 June 2014 diff hist +7 Thetas,Tajima,Neutrality tests →Estimate Tajimas D and other statistics
- 12:5212:52, 30 June 2014 diff hist −1 Thetas,Tajima,Neutrality tests →Estimate Tajimas D and other statistics
- 12:5212:52, 30 June 2014 diff hist +1 Thetas,Tajima,Neutrality tests →Step2: Calculate the thetas for each site
- 12:5212:52, 30 June 2014 diff hist −2 Thetas,Tajima,Neutrality tests →Step 1: Finding a 'global estimate' of the SFS
- 12:5112:51, 30 June 2014 diff hist +7 Thetas,Tajima,Neutrality tests →Calculate the thetas for each site
- 12:5112:51, 30 June 2014 diff hist +4,293 Thetas,Tajima,Neutrality tests →Estimate Tajimas D and other statistics
- 12:4812:48, 30 June 2014 diff hist +26 Thetas,Tajima,Neutrality tests →Output of the .thetas.gz file
- 12:4512:45, 30 June 2014 diff hist +2 Thetas,Tajima,Neutrality tests →Output of the .thetas.gz file
- 12:4412:44, 30 June 2014 diff hist +6 Thetas,Tajima,Neutrality tests →Step 1: Finding a 'global estimate' of the SFS
- 12:4312:43, 30 June 2014 diff hist +1 Thetas,Tajima,Neutrality tests →Step 1: Finding a 'global estimate' of the SFS=
- 12:4312:43, 30 June 2014 diff hist +4 Thetas,Tajima,Neutrality tests →Example
- 12:4312:43, 30 June 2014 diff hist +48 Thetas,Tajima,Neutrality tests →Example
- 12:4112:41, 30 June 2014 diff hist −3 Thetas,Tajima,Neutrality tests →Output of the .thetas.gz file
- 12:4012:40, 30 June 2014 diff hist −21 Thetas,Tajima,Neutrality tests →Example
- 12:4012:40, 30 June 2014 diff hist +103 Thetas,Tajima,Neutrality tests →Example
- 12:3812:38, 30 June 2014 diff hist +1,060 Thetas,Tajima,Neutrality tests →Example
- 12:3612:36, 30 June 2014 diff hist +44 N Tajima Thorfinn moved page Tajima to Thetas,Tajima,Neutrality tests current
- 12:3612:36, 30 June 2014 diff hist 0 m Thetas,Tajima,Neutrality tests Thorfinn moved page Tajima to Thetas,Tajima,Neutrality tests
- 12:3312:33, 30 June 2014 diff hist −2 Thetas,Tajima,Neutrality tests →Sliding Window example
- 12:3212:32, 30 June 2014 diff hist +33 Quick Start →Finding the SFS
- 12:3112:31, 30 June 2014 diff hist +60 Quick Start →Finding the SFS
- 12:2912:29, 30 June 2014 diff hist −1 2d SFS Estimation No edit summary
- 12:2812:28, 30 June 2014 diff hist −4 2d SFS Estimation →Example
- 12:2712:27, 30 June 2014 diff hist +10 SFS Estimation →How to plot
- 12:2712:27, 30 June 2014 diff hist −1 SFS Estimation →Posterior of the per-site distributions of the sample allele frequency
- 12:2612:26, 30 June 2014 diff hist +5 SFS Estimation →Interpretation of the output file
- 12:2612:26, 30 June 2014 diff hist +5 SFS Estimation →Example
- 12:2612:26, 30 June 2014 diff hist −1 SFS Estimation →Options
- 12:2512:25, 30 June 2014 diff hist −1 SFS Estimation →Brief Overview
- 12:2512:25, 30 June 2014 diff hist −2 SFS Estimation →Brief Overview
- 12:2412:24, 30 June 2014 diff hist −3 MsToGlf →Two populations
- 12:2412:24, 30 June 2014 diff hist +5 MsToGlf →Two populations
- 12:2312:23, 30 June 2014 diff hist +5 RealSFSmethod →Likelihood of the SFS current
- 12:2312:23, 30 June 2014 diff hist +5 Fst PCA No edit summary
- 12:2212:22, 30 June 2014 diff hist +5 RealSFS →1d SFS
- 12:2112:21, 30 June 2014 diff hist −3 RealSFS →2dsfs
- 12:2112:21, 30 June 2014 diff hist −2 RealSFS →1d SFS
- 12:2112:21, 30 June 2014 diff hist −2 RealSFS No edit summary