Doubt about PGAP-X program and FASTA formats

Question

[Airam]

Hello

I'm new here and in bioiformatics. I'm aligning bacterial genomes to analyze and compare the core genome. I'm using PGAP-X at Windows. The software needs *.fna and *.ptt files to run, but when I go to retrieve the genomes (in this case, plasmid sequences), I can't download it in *.fna format, it only can be downloaded in *.fasta format. I know that both formats are the same, but this program didn't recognize *.fasta format. I tried to change the file extension to *.fna, but the format didn't change. The same happens with the *.ptt files, because NCBI post that this kind of files were replaced for something like "feature_tables", that have different formats.

Somebody could help me?

Thanks

[GenoMax]

.fna files are in the fasta format. You should be able to change the .fasta extension on your files to .fna. There should be no need to change format.

For aligning bacterial genomes you could also try Mauve.