Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.
RNAforester [options]/home/vimalinx/miniforge3/envs/bio/bin/RNAforesterreferences/help.md for complete options and usage details# 1) Align structures from an input file
RNAforester -f=structures.txt
# 2) Compute local structural similarity
RNAforester -l -f=structures.txt
# 3) Predict structures from sequences before aligning them
RNAforester -p -f=sequences.fa > forester.out
RNAforester -f=inputfile for basic structure alignment, or add -l for local similarity, -s for small-in-large, or -m for multiple alignment mode-p to predict structures from sequences when needed, or --score to compute only scores without alignment output-2d for PostScript 2D plots if alignment inspection is needed-pm, -pd, -bm, -br, etc.) significantly affect results—use defaults unless specific tuning is required-m), consider clustering thresholds (-mt, -mc) to control alignment granularity