The get.sharedseqs command takes as input a group file and list file, or a shared file. This requires making OTU tables.
Is there a way to check which sequences are shared between the groups, given only a groups file, names files, the corresponding fasta files but no list file?
Hmmm, good question. You could run count.seqs which will tell you the frequency of each sequence in each group as a big table. Then you could process that further in R/excel/whatever. You could probably also do dist.seqs with a ridiculously small cutoff, run cluster with the count_table and then run make.shared.