Competitive Microbial Interaction Prediction

I have a collection of microbial genomic sequences already organised in FASTA files, and I need the competitive interactions among these organisms predicted. The workflow must rely on NetMet (netmet-utils / netmet-predict modules) together with the Miscoto optimisation tool so that the final network reflects both metabolic complementarity and potential cross-feeding conflicts.

Here is the scope I have in mind:
• Ingest the FASTA datasets, annotate metabolic pathways (you may choose Prokka or an equivalent step if needed) and feed the resulting models into NetMet for preliminary interaction scoring.
• Refine the competitive interaction graph with Miscoto, tuning the optimisation parameters to highlight the strongest negative interactions.
• Provide a clear summary report that includes: the ranked list of competitive pairs or consortia, visual network files (GraphML or Cytoscape-ready), and a brief methods section so I can reproduce the pipeline on new genomes. All scripts, environment files, and command logs should be delivered alongside the results.

I will consider the job complete once I can rerun your code on an unseen FASTA set and obtain a comparable interaction matrix.