A pipeline for phylogenetic analysis of haplotypes from each of the methods using PhyML[1].
Create and activate the conda environment:
conda env create -f environment.yaml
conda activate phylo-analysis
Run the script for each patient and method separately:
snakemake -c8 --config haplotype_folder=[directory with haplotype fasta files] oldest_consensus=[fasta file outgroup sequence] output_dir=[output] --
[1]: Guindon S, Dufayard JF, Lefort V, et al. “New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0”. In: Systematic Biology 59.3 (2010). doi:10.1093/nar/gki352, pp. 307–21.