Missing documentation and examples throughout

[jasondk]

Things that are missing:

• an example codon_stationary_distribution file, and an example aa_fitness_distribution (In general, if there is an option to use a file, we must have an example and a description of the expected format of the file)
• instructions for the user to install all python3 and R dependencies
• some example command-lines to run in the README

[jasondk]

• Also, when trying to do a single locus simuation (-g 1 codon) - an error is generated saying that the genome length must be the same as the number of fitness profiles given. Since I was forced to give a minimum of 2 fitness profiles, i am forced to have a minimum genome size of 2 codons. Should allow the user to do a 1 codon genome
  Error message: Please ensure that when using a fasta file, the same number of fitness profiles are provided as the length of the genome in the fasta file. Exiting.
• In the help system, it says the starting sequence file should be in amino-acids. When this is provided, an error is generated saying that nucleotides are required