Use when analyzing RNA secondary structure landscapes to find local minima via gradient walks, generate barrier trees, or compute rates for kinetic modeling with treekin.
RNAlocmin [OPTION]... [FILE].../home/vimalinx/miniforge3/envs/bio/bin/RNAlocminRNAsubopt output.treekin.# 1) Derive local minima from sampled suboptimal structures
RNAsubopt -p 10000 < sequence.txt > suboptp.txt
RNAlocmin -s sequence.txt < suboptp.txt > locmin.txt
# 2) Emit barrier-tree style output
RNAlocmin -s sequence.txt -b < suboptp.txt > barriers.txt
# 3) Keep only minima above a barrier threshold
RNAlocmin -s sequence.txt --minh 1.5 < suboptp.txt > filtered_minima.txt
RNAsubopt -p <count> < sequence.txt > suboptp.txtRNAlocmin -s sequence.txt < suboptp.txt to compute local minima via gradient descent-b for barrier tree output or -r for rates generation if kinetic analysis is needed--minh to report only minima exceeding a specified energy barrier threshold-s is optional if sequence is first line of input--noLP with random walk (-w R) or shift move set (-m S)-p to provide previously found local minima output instead of recomputing from sequence