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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- Pages
- Main_Page#Overview|ANGSD overview
- Download_and_installation|Installation
- Quick_Start|Quick Start/Testdata
- Input|Input data
- filters | Filters
- snpFilters | snpFilters
- Population genetics
- SFS Estimation|SFS Estimation
- tajima|Thetas,Tajima,Neutrality test
- 2d SFS Estimation |(Multi) SFS Estimation
- Direct Ancestry | Direct Ancestry
- Population structure
- NGSadmix | Admixture
- Fst |Fst
- Abbababa |ABBABABA (D-stat)
- Abbababa2 |ABBABABA (multipop)
- Pbs | Population branch statistics (pbs)
- PCA | PCA
- PCA_MDS | PCA (sampling approach)
- LD | Linkage disequilibrium
- Medical genetics
- Association|Association
- IBD/IBS
- Relatedness | Relatedness
- HWE_and_Inbreeding_estimates|HWE and inbreeding with ngsF
- HWE_test | HWE test
- Genotype_Distribution | Genotype distribution
- Heterozygosity | Heterozygosity
- Summaries
- Contamination|Contamination
- Error estimation|Error estimation
- alleles_counts|Allele counts
- depth|Depth
- base_quality|Base quality
- fasta | Create Fasta file
- Mismatch | Mismatch
- SNPs and genotypes
- Genotype_likelihoods|Genotypes likelihoods
- Inferring_Major_and_Minor_alleles|Major and Minor
- Allele_Frequency_estimation|Allele frequencies
- Genotype_calling|Genotype calling
- Haploid_calling|Haploid calling
- SNP_calling|SNP Calling
- Output
- beagle_input|Beagle inputation
- Genotype_likelihoods#Output_genotype_likelihoods|Genotype likelihood files
- Plink |Plink
- Misc/util programs
- realSFS | realSFS
- msToGlf | msToGlf
- thetaStat | thetaStat
- supersim | supersim
- Program structure
- angsd structure |Introduction
- angsd_class | overview of class
- custom_start | getting started
- data_access | accessing core data
- custom_data | custom data containers
- print | printing results
- About ANGSD
- change_log|Version log
- citing_angsd|Citing angsd
- authors|Authors
- Bugs | Bugs
- navigation
- mainpage|mainpage-description
- portal-url|portal
- currentevents-url|currentevents
- recentchanges-url|recentchanges
- randompage-url|randompage
- helppage|help
- SEARCH
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