The repository to extract the number of possible and observed synonymous, APOBEC3-relevant and -irrelevant mutations.
Due to recent overhaul of API in BioSequences, please
make sure the package version is 3.X by using
pkg>add BioSequences@3
Python scripts are written in Python 3.7.4, and requires the following packages:
- Biopython
- pandas
- csv
Data preprocessing based on accession numbers.
accession.txt |> get_collection_dates.py |> collection_dates.csv |> access.jl |> data, metadata.csv
Run identify_genes.jl to annotate the genes based on the reference genome.
Run embedding.jl to generate pairwise alignment and data for further analysis.
Run statistical_test.jl to generate the results of statistical tests.
Run comparison.jl to identify the equivalent classes of genomes and generate a distance matrix of the equivalent classes.
Run molecular_clock.jl to generate the results of molecular clock analysis.