if LAUNCH_ANALYSIS
puts "f. analysis:"
Dir.chdir "#{hmm_name}/msa/"
- run_command "#{PF} -s"
+ run_command "#{PF} -b=1 -s"
Dir.chdir "../.."
Dir.chdir "#{hmm_name}/msa100/"
- run_command "#{PF} -s"
+ run_command "#{PF} -b=100 -s"
Dir.chdir "../.."
puts
end