Hi Joe! MAUVE alignment files are in XMFA format and are a little troublesome to convert (in my opinion). When I have done this in the past I used a script written in Perl by Lee Katz. I'm not aware of any other converters for XFMA files, but I wouldn't be surprised if some are out there... Hope that helps.

Seems like BioPerl accepts XMFA input file format. You can use Bio::AlignIO to convert it to other formats e.g. Phylip in order to use it with RAxML.

Full genome alignments are only easy to construct for smaller genomes e.g. viruses but extremely difficult to construct for large genomes e.g. bacteria (or eukaryotic sequences) because it's computationally demanding among other factors. You can read this paper by Croucher et al (methods section) to see if you could use a similar approach like the one they used to construct phylogenetic tree for 600+ bacterial genomes (without doing a whole genome alignment)