Thanks @thermokarst,
What I'd like to be able to do is import a sequence that is not aligned, but does contain gap characters. When retrieving reference sequences from BOLD, it's possible for a sequence to contain one or more gap characters like this:
> seq1
AAT-CGAAACAGA-TC
What's awful is that they aren't actually aligned! So, in order to use the fancy new tools available in RESCRIPt, I need to be able to import these raw sequences. Trying to import them as a regular FeatureType[Sequence] will fail, correct? Is there an option that allows for gap characters to be tolerated as sequence data?
Certainly, it's straightforward to remove these with other tools prior to importing in QIIME, but I wanted to check whether I could get these into QIIME straight from the BOLD downloads.
Thanks!