NR class representatives only for rRNA distance matrices

......@@ -23,3 +23,5 @@ scripts/*.sh
......@@ -8,6 +8,9 @@ FEATURE CHANGES
The LSU and SSU are now aligned with Infernal options '--cpu 10 --mxsize 8192 --mxtau 0.1', which is slow,
requires up to 100 GB of RAM, and yields a suboptimal alignment (tau=0.1 is quite bad), but is homogenous with the other families.
- The LSU and SSU therefore have defined cm_coords fields, and therefore distance matrices can be computed.
- Distances matrices are computed on all availables molecules of the family by default, but you can use statistics.py --non-redundant to only
select the equivalence class representatives at a given resolution into account (new option). For storage reasons, rRNAs are always run in
this mode (but this might change in the future : space required is 'only' ~300 GB).
- We now provide for download the renumbered (standardised) 3D MMCIF files, the nucleotides being numbered by their "index_chain" in the database.
- We now provide for download the sequences of the 3D chains aligned by Rfam family (without Rfam sequences, which have been removed).
- statistics.py now computes histograms and a density estimation with Gaussian mixture models for a large set of geometric parameters,
......@@ -23,7 +26,7 @@ FEATURE CHANGES
- New code file geometric_stats.py
- New automation script that starts from scratch
- Many small fixes
- Many small fixes, leading to the support of many previously "known issues"
- Performance tweaks
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