There are many software applications such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:
- Making maps of plasmids
- Annotating plasmids with common features
- Finding restriction sites
- Mapping Sanger sequencing reads
- Showing sequence, reverse complement of the sequence, translations in different frames
- Designing primers for specific applications (such as Gibson cloning)
Is there a tool that does functions such as these, but runs from a command line?
Note: My intent is not so much to get recommendations for what to use, but to get an idea of what software is currently available. Obviously there exist many CLI tools which can be made to serve also these purposes, up to and including general purpose text editors like
I'm interested in what effort has already been made to produce CLI software specifically intended for cloning (by which I mean the functions described above).