**Gap content for site-specific rate factor calculation**:

parameter range: [0, 1] or >=3

When this parameter is above or equals to 3:

If the number of residues in a site is no less than this parameter, site-specific rate factor is estimated for this site. Otherwise the rate factor at this site is 1.

When this parameter is between 0 and 1:

If the fraction of residues in a site is no less than this parameter, site-specific rate factor is estimated for this site. Otherwise the rate factor at this site is 1.

Default: 0.5. (Sites with gap fraction larger than 0.5 will not be included for site-specific rate factor calculation)