+ FileUtils.cp orig_input, "#{hmm_name}/#{orig_input}"
+ end
+
+ Dir.mkdir( hmm_name + "/msa" )
+ Dir.mkdir( hmm_name + "/msa100" )
+
+ FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+ FileUtils.cp "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}.fasta", "#{hmm_name}/msa100/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+
+ if File.exists?( TEMPLATE_FILE )
+ FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa/"
+ FileUtils.cp TEMPLATE_FILE, "#{hmm_name}/msa100/"
+
+ if LAUNCH_ANALYSIS
+ puts "f. analysis:"
+ Dir.chdir "#{hmm_name}/msa/"
+ run_command "#{PF} -s"
+ Dir.chdir "../.."
+ Dir.chdir "#{hmm_name}/msa100/"
+ run_command "#{PF} -s"
+ Dir.chdir "../.."
+ puts
+ end