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ACRs

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 sequences
  • cdhit.fasta: non-redundant set of sequences
  • mafft.fasta: mafft alignment
  • trimal.fasta: trimal trimmed alignment
  • iqtree.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.

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