Aside from the obvious difference in the naming of the file extension, how do these files actually differ? and how do I convert a .fas file to a .faa file?? Thanks 
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They are both FASTA files, no conversion need - just rename them if you need to.
The extension *.fas is a common shortening of *.fasta, also *.fa is quite common. These could be protein or nucleotide FASTA data.
The extension *.faa is used by the NCBI for FASTA Amino Acids, meaning this is a protein FASTA file.
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