PhyloEffects is a piece of software to reconstruct variant effect annotations in their phylogenetic context.
conda install -c bioconda gffutils==0.12 treetime==0.11.2 cyvcf2==0.30.28 pyranges==0.0.129
To run the example data navigate to the repository and run
python phyloeffects.py -a example_data/100_aln.fasta -r example_data/Pseudomonas_aeruginosa_PAO1_v2.fa -t example_data/100_rescaled.nwk -o example_data/phyloeffects -c example_data/100_pos_mapping.txt -g example_data/Pseudomonas_aeruginosa_PAO1_107_converted.gff
PhyloEffects was used to infer variant effect annotations for the Pseudomonas Census Paper (Weimann et al. 2024). Refer to the Zenodo repository for the full input data.