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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  • SFStools is now included in main ANGSD, no need for double keeping of annoying big files.
  • -filter is now called -sites, which makes more sense. Since it was a site filter
  • -realSFS is now called -doSaf, and the output is no longer called .sfs but .saf. Which makes more sense. It wasn't the site frequency spectrum but the sample allele frequencies
  • Program can now do ABBABABA and consensus fasta.
  • many internal changes and bug fixes, that should make little difference

Sorry for having to do these changes.