This program does Blastp onto multiple genbank files. Hit results are
	then alligned with muscle.
	Alignment is used to create a Neighbour Joining tree with muscle.
	Also, it searches for domains provided form a prosite database within
	the blast hits.
	Makes "results" directory which has a directory for each query protein
	(same name) and contains the following:
	- A fasta file with the query sequence.
	- Blast hits in a fasta file with name "blast_query.fa".
	- Complete sequence looked onto converted gbk from blast hits with name
	  "blast_complete_query.fa"
	- A N-J tree in newick format with the name "tree_query.fa".
	- A file with all the found protein domains with the name 
	  "prosite_query.txt". Contains blast hit name, prosite name,
	  accession, description, pattern and blast hit domain.

	Also makes a data/gbk_to_fasta directory that has all genebank files
	fused into a file with fasta format (gbk_converted_to_fasta)
	Alignment is stored in the temporary directory /tmp/muscle_out

	-h: help
	- genebank_directory: a directory that has one or more genebank files
	  with .gbff termination to be used as subject
	- query_fasta_file: a single file that has one or more query in fasta
	  format
	- prosite_database.dat: a file that has protein domains in prosite
	  format 
	- identity_cutoff: a number, may be decimal, blast hits with lower
	  identity are filtered
	- coverage_cutoff: a number, may be decimal, blast hits with lower
	  coverage are filtered