Bigslice

Latest version: v2.0

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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](https://github.com/althonos/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)

2.0.0rc

- 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

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

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

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.

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