Open ritafonso opened 2 years ago
Dear @ritafonso,
MEME and FUBAR are designed to work with fixed differences (not within-population polymorphism). That said, people commonly analyze some types of data (e.g. viruses or bacteria) where each sequence is one individual. Not sure what you mean by separeted phased alleles
.
Also, be advised that neither MEME nor FUBAR will work particularly well on small datasets (6 sequences). Consider using a recent modification of FEL.
Best, Sergei
Dear @spond ,
thank you very much for your quick response!
By separed phased alleles I mean the two alleles of a diploid sequence of a gene, but I guess that doesn't matter if the software works only with fixed differences.
How many sequence would you consider a large dataset, worth of using MEME or FUBAR?
Best regards,
Rita
Hi,
I'm using MEME and FUBAR in a dataset of 6 species, but I'm most interested only in one. I'm wondering if for that species I should include all the individual's sequences that I have or just a consensus. Also, should I use separeted phased alleles or just a consensus sequence for each species?
Thanks in advance, Rita