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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.
Updated