What is a good multiple alignment of large genome sequences when working with limited hardware?
First of all, do not, I repeat not, use ClustalW. That is horribly out of date and was never very good to begin with1. It was just the first to become common. At least use ClustalΩ. Anyway, while I haven't done much aligning in the past few years, back when I did, I got the best speed/quality ratio from MAFFT. 

MAFFT has been used in various sequencing projects and can deal with whole genomes easily. Whether or not it will run correctly on your machine depends on the specs of your machine, of course. However, it should be considerably more efficient than clustalW, although not necessarily more than muscle. 

Before doing any of this though, are you sure you need to align whole genomes? Could this be an XY problem? You might want to consider posting a new question here and explaining what your final objective is. Also, if these are published genomes, you might be able to find an existing alignment. 

If you really do need to run a whole genome alignment and your machine can't use MAFFT or muscle or any of the other modern aligners, you need a new machine. No matter how efficient your aligning algorithm, a genome is a lot of data and you need a strong machine with serious RAM for it. If you are on a *nix machine, you could ask about how to create a swapfile to increase your memory on Unix &amp; Linux.



1Don't get me wrong, it was state of the art and everything back in the day, but the state of the art wasn't very good, that's all.