aliFreeFoldMulti

What is aliFreeFoldMulti ?

• Alignment-free approach to predict secondary structure.
• Computes a representative structure for each sequences from a set of homologous RNA sequences.
• Computes a stems-alignment using the stems from the 25 first suboptimal secondary structures.
• Using the stems-alignment, compute the closest suboptimals from the suboptimal secondary structures for each sequence of the set of homologous RNA sequences.

How to run aliFreeFoldMulti

1. Download the source code.
2. /path_to_aliFreeFoldMulti_folder/main.py path_to_input_file {"first" | "last" | "best" | "all"} path_to_output_folder {"true" | "false"} {"true" | "false"}

• The input file must be ".fa" or ".fasta".
• Select one of the options for the stems-alignment algorithm: {"first" | "last" | "best" | "all"}.
• The output folder must be existing, it will not be created during the execution.
• The fourth option is to get or not the result file containing the centroids.
• The fifth option is to get or not the result files, one containing the stems-alignment and the other the closest suboptimals.