seqret embl:KM577634[68:1025] rat.fa
     cat rat.fa >> rna12.fasta
     muscle -align rna12.fasta -output rna12.afa
     python reformat.py
     fastme -d -i rna12.phy -o rna12.tre
     
     
     fastme -d -i rna12.phy -o rna12_bootstrap.tre -b 100
     fastme -dp -i rna12.phy -o rna12_bootstrap_pdist.tre -b 100
     
     reformat.py:
     	from Bio import AlignIO
     inh = open("rna12_nei.afa", "r")
     outh = open("rna12_nei.phy", "w")
     alignment = AlignIO.parse(inh, "fasta")
     AlignIO.write(alignment, outh, "phylip-relaxed")
     inh.close()
     outh.close()