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Tassel 5 Source / UserManual / Load / DataFAQ

1. How do you load SSR data?

SSRs are no longer supported specifically in TASSEL 5. TASSEL 4 supported them. This has to do with the memory efficiency of various data structures. One strategy is to recode the SSRs as SNPs, note collapsing the rare alleles is generally a good idea anyhow.

Code the SSRs alleles as follows:

  • Most common = A
  • 2nd most common = C
  • 3rd most common = G
  • 4th most common = T
  • 5th most common = +
  • All other alleles = - (dash)

Also any allele class with less than 10 taxa(individuals) should be included in the all other alleles class.