This isnt something crucial, just a suggestion: Is it possible to add group and name optional parameter to chop.seqs()? The way it is now it cuts sequences at set length and when short=F it discards all shorter sequences. Chops.seqs generates accnos file of the discarded sequences and you can use remove.seqs() to remove entries in .names and .groups but it s not much fluid 
This will be part of 1.31.0. Thanks for the suggestion!