Ngsphy

Changed functionality of the script. It now takes a single prefix and a project
folder, iterates over all the species trees, takes the fasta files with the
selected prefix and mates those files outputting them into a folder
inside the project folder called INDIVIDUALS

Generated "individuals" go now into a "individuals" folder, organized by
Species tree ID and Gene Tree ID, all files in a single folder is at all
manageable.
Reformatted the names of the generated files.
Mating file "db", now has an extra field. This field identifies the individual.
Single output folder for all the sequences.
All individuals have a specific name which allows not to get confused.

Getting information about the species tree that have even/odd number
of individuals per species

It is possible to write different number of output according to
preferences.

Run is no longer finished if a replicate has no sequences
it will just skip it.

Enhanced logger