d4cb6f78 · delete unused cm_coords at updates ·
April 2021 Update

v 1.5 beta, April 2021


  • New option --stats-opts="..." allows to pass options to the automatic run of statistics.py (when -s is used)
  • Removed support for 3'->5' Rfam hits, they are now completely ignored. They concern the opposite strand, which is unresolved in 3D.
  • Removed PyDCA, which is outdated and introduces dependencies conflicts. Code may be adapted later.
  • A new column in align_column table, index_small_ali, gives the index of the nucléotide in the "3d only" alignment.
  • 3D distance matrices are now computed only for match positions (match to the covariance model)


  • Corrected a bug which skipped angle conversions from degrees (DSSR) to radians if nucleotides where renumbered.

v 1.4 beta, March 2021

Khodor Hannoush joins the development of RNANet.


  • SINA is now used only if you pass the option --sina, Infernal is used by default even for rRNAs.
  • A new option --cmalign-opts="..." allows to customize your cmalign runs, e.g. with --cyk. The default is no option.
  • RNANet makes use of PyDCA to compute DCA-related features on the alignments (descriptions to come in the Database.md)
  • statistics.py now fully supports the computation of 3D distance matrices, with average and standard deviation by RNA family
  • Now RNANet considers only the equivalence class representative structure by default. To consider all members of an equivalence class (like before), use the --redundant option.


  • cmalign is not run with --cyk anymore by default, and now requires huge amounts of RAM if launched with the default options.
  • Moving to a 60-core/128GB server for our internal runs.