This code repository accompanies the manuscript

*An Evolutionary Trace method defines functionally
important bases and sites common to RNA families*

/work in progress/

There are two component of interest

1. ET program (ET_RNA_ms/et_bin/wetc) stand-alone C binary that produces ET ranking given a MSF alignment should run on any system with a compatible compiler

   To run:

   1. In terminal, navigate to ET_RNA_ms/et_bin/

   2. Ensure the program runs by typing "./wetc - help"

   3. To score an RNA aligment, type

      ./wetc -p [aln_path] -x [query_seq_name] -dnaet -realval -o [output_name]

      -p path to MSF alignment -x name of the query sequence as it appears in the alignment -dnaet flag to enable non-protein scoring -realval flag to run rvET scoring -o base name for output files (can direct into dir '-o dir_path/basename')

2. Ribosome Example (ET_RNA_ms/ribosome_example) example of ET application using the 16S rRNA alignment, including the ET trace, and z-score computations uses wetc to produce ranking, but wrapped in MATLAB otherwise

   To run:

   1. Launch matlab
   2. Navigate in matlab console to ET_RNA_ms/ribosome_example
   3. Type 'ls' (no quotes) to examine contents of folder, there are 3 scripts of interest trace_alignment.m traces the 16S alignment measure_et_structural_clustering calculates ET clustering in the 16S structure measure_et_prediction_accuracy calculates ET overlap with know functional sites in 16S
   4. Execute these 3 scripts in order
   5. Results and plots will be in the results/ and visualizaion/ folders