d4cb6f78 · ·
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
- 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- Removed PyDCA, which is outdated and introduces dependencies conflicts.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
- cmalign is not run with
--cykanymore 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.