A collection of Python scripts extending the functionality of Biopython
git clone https://github.com/PoonLab/Bioplus
pip install -e Bioplus
add_dates.py- IN PROGRESS - Use metadata to relabel sequences in the associated FASTA file. Optionally, use the dates to down-sample the sequences to a target size so that dates are evenly distributed.dist.py- Calculate a k-mer distance (Euclidean, spectrum kernel), p-distance or Jukes-Cantor corrected distance for an alignment of nucleotide sequences.get_metadata.py- Retrieve metadata (e.g., sample collection dates) associated with sequences in the input file, based on their respective NCBI Genbank accession numbers.permute_fasta.py- Random permutation of FASTA file. This script reads a FASTA-formatted file containing aligned sequences and applies a random permutation of alignment columns (nucleotide sites), writing the result to a new FASTA file. This has the benefit of providing some data security (by scrambling the original sequences) while preserving information about evolutionary relationships.prunetree.py- Down-sample a sequence alignment by building a tree and progressively removing the shortest tips until only a target number of tips remain. The tip labels are used to select sequences from the alignment.sampler.py- Reduce the number of sequences in a file by random sampling.