load the phenotype data for ballgown
You can easily do it via Notepad++ or even Excel. Just don't forget to save the output file as a .csv file (comma-separated value). 
The info inside should look like (my working example):

id,state
lar_control141,control
lar_control142,control
lar_control143,control
lar_probiotic142,probiotic
lar_probiotic143,probiotic
lar_probiotic144,probiotic
lar_probiotic145,probiotic
lar_probiotic146,probiotic


That should work