Software/Tool for aligning multiple nucleotide viral genome sequences (n=15; 300kb in length) while maintaining features/annotations?

Question

[Olivia]

HI,

I am looking for a software program or tool that will enable multiple sequence alignment of ~15 viral nucleotide genome sequences of length 300kb. These sequences are available for download as .gbk files but I can't find anything that can align .gbk files and maintain the gene annotations.

Is there a way to do this using a feature table that could be re-associated with the original sequence once aligned?

Tools/software that are linux based would be best so that I could run it on our HPC.

Any suggestions or other ways of doing this would be appreciated!

Thanks, Olivia