Add all needed infrastructure for MSAprobs and GLprobs

[jabaws.git] / website / prog_docs / glprobs.txt

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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)
+*************************************************************************
+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 
+