I'm new to this community, so firstly I ask you to understand if I make any mistakes regarding how this forum works and also for my english (it's not my first language). So... I have some output files from PGAP (pan-genomes analysis pipeline), this tool allows me to verify the core genome, accessory genes and species-specific genes. I'm currently working with bacteria (3 species from genus Proteus) and I need to get all the sequences from the core genome and make it all into a multiFASTA file (to use as input to Vaxign). The problem is that PGAP doesn't generate FASTA files, instead the output files formats are EMBL, .nuc, .pep and other formats. Can I convert these EMBL files into a multiFASTA file? I tried using seqretsplit to split the EMBL file into multiple EMBL files with one sequence each (to convert them to FASTA and merge them right after), but even after reading the manual I couldn't figure out how to do it properly (it was only making a file with a single sequence). Is there any other way to create a multiFASTA file? Can I use seqretsplit to convert the EMBL file to a multiFASTA file? If so, how do I do that? I tried using online converters but I guess the files are too big. I apologize for my lack of computational skills, I'm new to the bioinformatics field. Thanks in advance!