1 ************************************************************************
2 MSAPROBS is a open-source protein multiple sequence alignment algorithm
3 based on pair hidden markov model and partition function postirior
4 probabilities. If any comments or problems, please contact
5 Liu Yongchao(liuy0039@ntu.edu.sg or nkcslyc@hotmail.com)
6 *************************************************************************
8 msaprobs [OPTION]... [infile]...
11 Align sequences in multi-FASTA format
13 -o, --outfile <string>
14 specify the output file name (STDOUT by default)
15 -num_threads <integer>
16 specify the number of threads used, and otherwise detect automatically
18 use CLUSTALW output format instead of FASTA format
20 -c, --consistency REPS
21 use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
23 -ir, --iterative-refinement REPS
24 use 0 <= REPS <= 1000 (default: 10) passes of iterative-refinement
27 report progress while aligning (default: off)
30 write annotation for multiple alignment to FILENAME
33 print sequences in alignment order rather than input order (default: off)
35 print out version of MSAPROBS