Generate Ks plots using bottom-ranked reciprocally retained gene families

[Cecilia-Sensalari]

Generate Ks plots using bottom-ranked reciprocally retained gene families
This PR adds the possibility to run the reciprocal retention Ks pipeline for the bottom-ranked GFs instead of the top-ranked GFs.
This is done for comparison purposes with the top-ranked GFs, which we showed being good in narrowing down Ks distributions to WGM-derived signal. The expected distribution derived from bottom-ranked GFs shouldn't retain very well WGD-derived signal (so, unclear peaks), especially if peaks as very old.
The first results using the palm example dataset confirm this expectation.

Detailed description of changes:

• Add parameter use_bottom_gfs_instead_of_top in expert configuration file to toggle the use of bottom-ranked GFs instead of top-ranked GFs (default); boolean bottom variable has been added to the code to handle this switch.
• The log lines now print either "top" or "bottom", instead of hard-coding "top" (var. top_or_bottom)
• Existing variable top is renamed as num_gf because it actually contains the number of (top or bottom) GFs to be considered from the 9178 GFs ranking.