mgcluster input?

Commands in mothur
1

Hi Pat,
I’m trying to use mgcluster and have a couple newbie questions.

What exactly is the input for mgcluster. It’s a blast file - but what format? XML, tabular, etc?

Also, should the input file just be the sequences all blasted against each other? Or should it be all genes found by something like glimmer blasted against each other?

Thanks

2

Hi Prohan,

The input is the blast table -m 6(?) and yes it should be an all vs. all blast of pre-called orfs. We’re still trying to figure out how to wrap our heads around doing it without calling orfs first.

Pat