seqret @clpx_mid.list clpxm.fasta			
	muscle -align clpxm.fasta -output clpxm.afa
	python reformat.py
	fastme -pm -i clpxm.phy -o clpxm.tre
          
	reformat.py:
     		from Bio import AlignIO
     		inh = open("clpxm.afa", "r")
     		outh = open("clpxm.phy", "w")
     		alignment = AlignIO.parse(inh, "fasta")
     		AlignIO.write(alignment, outh, "phylip-relaxed")
     		inh.close()
     		outh.close()