RemEff: Clusters, MSAs and HMMs of fungal proteins

Complete clustering dataset from the remeff paper.<br>"clusters.tsv" gives the IDs of cluster centroids (representative members), and cluster members in the first and second columns, respectively.<br>"remeff_fasta.ff{data,index}" gives the multiple sequence alignments of all clusters presented in "clusters.tsv"The ffdata, ffindex format (https://github.com/soedinglab/ffindex_soedinglab) is formatted to be used by the HHsuite3 software (https://github.com/soedinglab/hh-suite)<br><br>"remeff_a3m.ff{data,index}" gives the multiple sequence alignments from "remeff_fasta" but in a3m format, and is enriched with partial alignments of sequences from uniprot, and has some redundancy removed to avoid biasing HMM construction.<br>"remeff_hhm.ff{data,index}" gives the HHsuite3 HMM representations of all clusters. This file is build from "remeff_a3m".<br>"remeff_cs219.ff{data,index}" gives the HHsuite3 prefiltering dataset for all clusters. This file is build from "remeff_a3m".<br><br>To run searches against this database using hhsuite, you need the six files matching the pattern remeff_a3m*, remeff_cs219*, and remeff_hhm*.<br><br>You need to uncompress them using gzip or pigz.