Future functionality

Tools we may integrate into CompareM2 when time allows.

Per-genome analyses

• AlphaFold — Neural network protein structure prediction.
• DRAM — Metabolic interpretation via distilled genome annotations.
• Oriloc — Replication origin identification in chromids.
• RFplasmid — Plasmid identification using pentamer random forests.
• distillR — Graph-based metabolic capacity indices from functional annotations.

Cross-genome analyses

• GC3-profiling — Synonymous GC-content distribution fingerprinting.
• Recombination detection in core genome using Bruen's PHI statistic or ClonalFrameML.
• Identification of horizontally transferred genes.

Please open an issue if you have ideas or requests.