This repository hosts the bioinformatic analysis worklow used in Oppermann et al, Robust Optogenetic Inhibition with Red-light-sensitive Anion-conducting Channelrhodopsins, eLife.
The snakemake-based code for the workflow is under workflow/. The dependencies are under conda control (snakemake --use-conda), see workflow/envs. The analysis files are under analysis/, in particular ACRs/analysis/pdb contains the output files for the structural alignment (sequences.aln is the main output) and analysis/all hosts the various files generated for the phylogenetic analysis:
sequences.fasta: unaligned sequencescdhit.fasta: non-redundant set of sequencesmafft.fasta: mafft alignmenttrimal.fasta: trimal trimmed alignmentiqtree.treefile: the phylogenetic tree from iqtree with ultrafasta bootstrap support values
The metadata for the sequences can be found in metadata/Channelrhodopsins_Updated_List.xlsx which is a snapshot of the Catalogue of Natural Channelrhodopsins.