clustrX: Reproducibility Package and Benchmarks

This package contains the source code, raw datasets, and replication scripts to reproduce the benchmarks and figures of the paper submitted to Nature methods: 'clustrX enables accurate and robust protein clustering through community detection in homology networks'. Detailed step-by-step instructions for conda environment setup, compiling SiLiX, and running each benchmark (Pfam, short peptides, scalability, and twilight-zone simulations) are included in the README.md file inside the downloaded archive.