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IncaRNAtion Launch the script /src/IncaRNAtion.py, the options are below. The library MPMATH is highly recommanded for long sequences:https://github.com/fredrik-johansson/mpmath/ The script /src/incarnation_3.py is a python3 version of the IncaRNAtion software. Required: -d <file_path> A file containing the target secondary structure and an optional MSA -a <float> The value of alpha, between 0 and 1. 1 takes only into account the secondary structure, 0 only the MSA Optional: -m <int> The max penality for an invalid base pair, -1 for infinity -b <int> print 'n' stochasticly backtracked sequences -no_profile <> Doesn't output a profile -s_gc <target_gc> <nb_samples> Sampling sequences with a 0<=target_gc<=1 and a given number of samples -gc_sec_struct <> Only the nucleotides with an interaction in the secondary structure will be considered for the GC content -gc_max_err <float> Max error from GC target allowed in sample, default 0.1 -gc_data <file_name> Create a file with the given name, will print to it a first line the weight of 'C' and on the next the list of sampled GC content -t <float> The temperature (default 310.5K) -c <IUPAC sequence> An IUPAC sequence to constrain the outputed sequences -p <file_path> A data file with starting RNA profile (i.e. every lines contains nucleotides probability in order: 'ACGU') e.g. python IncaRNAtion.py -d data.txt -a 0.5 -m 20 python IncaRNAtion.py -d data.txt -a 1 -m 20 -no_profile -s_gc 0.5 100 python IncaRNAtion.py -d data.txt -a 0.5 -m 20 -b 5 -no_profile """