[WARNING]: 182190 of your sequences generated alignments that eliminated too many bases,

Commands in mothur
#1

Hi there, im having trouble figuring out why so many sequences had bases eliminated. I have attached a google doc with the pipeline and the outputs from the corresponding line of input coding which can be found here.

Any advice would be appreciated!

#2

Hi SNOSO,

I don’t have access to your google doc. Could you just post the output that mothur put to the screen?

Pat