Add option to only use genes that are found in all of the proteomes

[iimog]

From the discussion in #20 it became clear that this option would be beneficial.

Currently there is a fixed cutoff for the minimum number of proteomes for a gene to be considered (2). So only genes found in less than two proteomes are discarded from further analyses.
This cutoff could be generally configurable (--min-proteomes, with a default value of two). Another convenience parameter (--all-proteomes) can be introduced that sets --min-proteomes to the number of proteomes given.

• Add parameter to perl script
• Add option to java interface