PLMView sequence and annotation dataset

This repository contains all input files used to generate the trees presented in the PLMView paper. It also includes trees generated using PLMView, SSN with linkage clustering, averaged PLM embeddings with Ward clustering, and trees based on the metrics used by FANTASIA. iTOL annotation files are provided for each dataset. Each compressed folder corresponds to a protein family analyzed with PLMView and contains four or five subfolders:- Input protein sequences- Generated trees - iTOL annotation files- PLMView representation-space matrix- Functional Determinants analysis results, when available