Bugfixes on v2

• contain several important bugfixes that gets merged after the v2.0.0, please use this version if you are still on 2.0.0

Version 2.0.0

• Clustering now uses cosine-like (via l2-normalization) distances (as in https://www.nature.com/articles/s41564-022-01110-2)
• pHMM databases have been updated to PFAM 35.0
• BGC class definition has been updated to antiSMASH v7.0.0
• Switching from HMMER to pyHMMER (speed-ups, can now be fully installed via pip)
• General speed improvement
• Ability to export pre-calculated BGCs and GCFs table into TSVs (use --export-csv parameter)

BiG-SLiCE v2.0.0 (release candidate)

• Clustering now uses cosine-like (via l2-normalization) distances
• pHMM databases have been updated to PFAM 35.0
• BGC class definition has been updated to antiSMASH v7.0.0
• Switching from HMMER to pyHMMER
• General speed improvements

Version 1.1.1

Several minor updates:

• fix behavior when under compute clusters environment (thanks to @waltersom)
• accept antiSMASH v6 regiongbks as input
• displays the loaded HMM database release version
• --complete mode no longer treats MIBiG BGCs as complete BGCs
• small improvement to BIRCH clustering algorithm
• fix parsed regiongbk paths folders losing their first characters
• change default --n_ranks to 1

Version 1.1.0

• bugfix for download_hmmdb script and taxonomy parser module
• SQLite schema improvement (speed up on visualization output)
• added ASCII-art for help text

Version 1.0.0

The very first (production-ready) release of BiG-SLiCE. Contain the core clustering pipeline, standard pHMM models and the accompanying visualization engine.