jalview is best tool for MSA. Give a try, you will like it

We have quite a lot of them packaged in Debian, plus the EMBOSS package that can convert multiple sequence alignment outputs from one format to the other.

I guess you have quite some options. I personally use muscle most of the time.

Jalview is a free protein and nucleic acid sequence alignment visualisation software. It can be launch from http://www.jalview.org/. There are several Jalview 'how-to' videos on the Jalview YouTube training channel (https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw). I recommend the one on 'Saving alignments, trees, 3D structures, annotations and projects in Jalview' at https://youtu.be/zXrOlOsyZdc.

Multiple Sequence Alignment Tools You should consider the length and number of sequences to see if the tool can handle it. Personally, I would use clustal, and parse the .aln file into a fasta.

Jalview is great, but focuses on proteins. Have a look at Base-By-Base: https://virology.uvic.ca/virology-ca-tools/base-by-base/

This can handle genes, proteins, viral genomes (up to 400 kb). It has a different set of modules than Jalview.

It makes editing MSAs easy and displays the differences between sequences so that it's easy to use.

It has the ability to find SNPs that are in seqs A, B and C, but not in seqs D or E. (and more complicated logic)