Similarity between the human genome and archea genome in deep sea hydrothermal vents?
To achieve whole genome alignment between a genome as large as a human, and as small as an archea organism, is possible, but in the end, you'll have to strain your eyes to see patterns. The archea genome is about 1-5 million bp long, whereas the human genome is about 3.3 billion bp long (that's a thousand times too large).

In practice what this means is that you may or may not have small islands of similarity, in vast regions of emptiness.

Nevertheless, you can align whole genomes using the MUMer tool (http://mummer.sourceforge.net/). The white paper is here 
Delcher, Arthur L., et al. "Alignment of whole genomes." Nucleic acids research 27.11 (1999): 2369-2376.

You might also be interested in reading this:

Wei, Liping, et al. "Comparative genomics approaches to study organism similarities and differences." Journal of biomedical informatics 35.2 (2002): 142-150.