CGG toolkit: Software components for computational genomics.

Acknowledgements: We recognize multiple contributions by former members of the CGG and other colleagues who have contributed to the testing and use of the mentioned software. Most of the original development was by AJE and CAO (DifFuse, GeneRAGE, Tribe-MCL), AJE and VJP (GeneCAST) and AJE and CAO (CoGenT/++, TRIBES/OFAM). Other members of CGG who have contributed to additional components (BioLayout, MagicMatch) can be identified as co-authors in the original manuscripts. DA and PJJ have acted as curators and test-drivers for CoGenT and CoGenT++ frameworks. DV and CAO reimplemented and launched the GitHub versions as v1.0.1 and tested clustt_utils. IB with II (specifically GeneCAST, DifFuse) and CK with AC (specifically MagicMatch, cogent_utils) helped with testing and validation phases of the current versions.Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release