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.
Example of a covariance file
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1 0 0 1
1 0.1 0 0
2 0 1 0
2 0 1 0
2 0.1 0 1
1 0 0 1
1 0.3 0 0
2 0 0 0
1 0 0 0
2 0.2 0 1
1 0 1 0
1 0 0 0
1 0.1 0 0
1 0 0 0
2 0 0 1
2 0 0 0
2 0 0 0
1 0 0 1
1 0.5 0 0
2 0 0 0