Can we align a .fna file with .fastq file in multiple sequence alignment using Biopython?
Please be more specific, why do you want to do that? The first question should be if it makes sense, and it most likely doesn't.
This question can be answered by just runnning your python program and seeing if you get any errors..I haven't tried it but you may definetly get errors because .fna just contains the nucleic acid sequence whereas fastq contains your sequence with their corresponding quality scores..
To convert fastq to fasta format, check this out- Fastq Convert To Fasta
Convert fastq to fasta and then align them together (whatever you're up to... ^^)