Workflow about phylogeny tree using virus whole genome sequence

Question

[phswin92]

Hello, I have a question about the virus analysis workflow.

I have 10 full-genome sequence fasta files, a one fasta file has multiple reads for a virus. If I try to MSA and draw a phylogeny tree, do I have to have 10 fasta files as one fasta file? The reads in one fasta file must be a one-line sequence, but how can I do this process?

Could you briefly tell me about the workflow for creating a phylogeny tree using the virus whole-genome sequence?

Best,