FAQ

Q: Something weird is happening, e.g. program is crashing with my data. What should I do?
A: Please add --debug to the command line (or --parsing-debug if some files were not read correctly) and post the details in Issues.

Q: How to get representative protein ids of flanking genes for a hotspot?
A: Each hotspot includes an attribute called conserved signature, which contains the protein IDs of representative sequences for protein families that are highly conserved as flanking genes (found as flanking genes in over 75% of hotspot islands). Starting with iLund4u version 0.0.8, this information is available in the conserved_signature column of the hotspot_annotation.tsv file.

Q: How to use pre-defined protein clusters instead of mmseqs clustering step?
A: Starting with 0.0.10 version iLund4u has --pclt, --protein-clusters-table <path> parameter that takes as input path to a table with predefined protein clusters. Format: mmseqs-like cluster table (two columns, first - cluster_id; second - protein_id; without header).

Q: How to use pre-defined proteome (sequence/contigs) communities instead of network-based Leiden community detection algorithm?
A: Starting with 0.0.10 version iLund4u has --pcot, --proteome-communities-table <path> parameter that takes as input path to a table with predefined proteome communities. Format: mmseqs-like cluster table (two columns, first - community_id; second - proteome_id; without header). In addition, it's possible to force iLund4u to consider all contigs as members of one community (pangenome-like mode). For that, simply apply -spc, --single-proteome-community parameter.