RemEff: Clusters, MSAs and HMMs of fungal proteins

Complete clustering dataset from the remeff paper.
"clusters.tsv" gives the IDs of cluster centroids (representative members), and cluster members in the first and second columns, respectively.
"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)

"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.
"remeff_hhm.ff{data,index}" gives the HHsuite3 HMM representations of all clusters. This file is build from "remeff_a3m".
"remeff_cs219.ff{data,index}" gives the HHsuite3 prefiltering dataset for all clusters. This file is build from "remeff_a3m".

To run searches against this database using hhsuite, you need the six files matching the pattern remeff_a3m*, remeff_cs219*, and remeff_hhm*.

You need to uncompress them using gzip or pigz.