I want to calculate alpha diversity for a list of taxa. I can make a file that has the desired taxa, feed that into a for loop something like this:
for t in taxa.file; do mothur #get.lineage(shared=final.shared, constaxonomy=final.cons.taxonomy, taxon=$t); summary.single(shared=current, size=1000, n=100); done
But, that would overwrite the new shared and alpha div files each time. Right? Is there another way to do this?