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.