Multiple Sequence Alignment of Bacterial Genomes

Question

[Optimist]

Hi All,

I have a couple of queries regarding Multiple Sequence Alignment.

1. I have downloaded Genomes in fasta format from NCBI. Some are Complete and rest are Scaffolds and contigs.
2. So how to use these files for Multiple Sequence alignment?
3. Is there any requirement for concatenating them in order to use for MSA?
4. Which tool you feel is the best for this purpose?

Thanks a lot.

Chanakya