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	MSAPROBS is a open-source protein multiple sequence alignment algorithm
	based on pair hidden markov model and partition function postirior
	probabilities. If any comments or problems, please contact
	Liu Yongchao(liuy0039@ntu.edu.sg or nkcslyc@hotmail.com)
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Usage:
       msaprobs [OPTION]... [infile]...

Description:
       Align sequences in multi-FASTA format

       -o, --outfile <string>
              specify the output file name (STDOUT by default)
       -num_threads <integer>
              specify the number of threads used, and otherwise detect automatically
       -clustalw
              use CLUSTALW output format instead of FASTA format

       -c, --consistency REPS
              use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

       -ir, --iterative-refinement REPS
              use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement

       -v, --verbose
              report progress while aligning (default: off)

       -annot FILENAME
              write annotation for multiple alignment to FILENAME

       -a, --alignment-order
              print sequences in alignment order rather than input order (default: off)
       -version 
              print out version of MSAPROBS