How to reduce the redundance in proteomic dataset

Question

[luileo_10]

Hello, I am working with several sets of proteomics, one of the steps I need is to reduce redundancy to be able to move on to the next analyses. However, I wanted to know what software to use on Windows, I have seen that there is cd-hit, does anyone have experience with that?

[GenoMax]

Not for Windows (unless you can use WSL2 on Win 11) MMSeqs2 (LINK) is likely the current state of the art for clustering at this time.

This paper describes a pipeline that UniProt uses for their proteomes but it does not appear to be accessible for end-users directly: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199198/