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.
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** SNP_calling|SNP Calling | ** SNP_calling|SNP Calling | ||
**tajima|Thetas,Tajima,Neutrality test | **tajima|Thetas,Tajima,Neutrality test | ||
* Population structure | |||
** NGSadmix | Admixture | |||
** Fst_PCA |Fst & PCA | |||
** Abbababa |ABBABABA (D-stat) | |||
* Output | * Output | ||
** beagle_input|Beagle input files | ** beagle_input|Beagle input files | ||
| Line 36: | Line 42: | ||
** filters | Filter output | ** filters | Filter output | ||
** Plink |Plink | ** Plink |Plink | ||
* custom analysis | * custom analysis | ||
** angsd_class | overview of class | ** angsd_class | overview of class | ||
| Line 42: | Line 49: | ||
** custom_data | custom data containers | ** custom_data | custom data containers | ||
** print | printing results | ** print | printing results | ||
* navigation | * navigation | ||
Revision as of 18:36, 2 December 2013
- Pages
- Main_Page#Overview|Overview
- Download_and_installation|Installation
- Quick_start|Quick start
- Input|Input data
- change_log|Version log
- citing_angsd|Citing angsd
- authors|Authors
- Bugs | Bugs
- Count based summaries
- alleles_counts|Allele counts
- depth|Depth
- base_quality|Base quality
- alleles_counts|Allele counts
- Methods
- realSFS|SFS estimation
- Genotype_likelihoods_from_alignments|Genotypes likelihoods
- Inferring_Major_and_Minor_alleles|Major and Minor
- Error estimation|Error estimation
- Allele_Frequency_estimation|Allele frequencies
- HWE_and_Inbreeding_estimates|HWE and inbreeding
- fasta | Create Fasta file
- Association|Association
- Genotype_calling|Genotype calling
- SNP_calling|SNP Calling
- tajima|Thetas,Tajima,Neutrality test
- Population structure
- NGSadmix | Admixture
- Fst_PCA |Fst & PCA
- Abbababa |ABBABABA (D-stat)
- Output
- beagle_input|Beagle input files
- beagle_output | Beagle Output files
- Glf_files|Genotype likelihood files
- filters | Filter output
- Plink |Plink
- custom analysis
- angsd_class | overview of class
- custom_start | getting started
- data_access | accessing core data
- custom_data | custom data containers
- print | printing results
- navigation
- mainpage|mainpage-description
- portal-url|portal
- currentevents-url|currentevents
- recentchanges-url|recentchanges
- randompage-url|randompage
- helppage|help
- SEARCH
- TOOLBOX
- LANGUAGES