Description:

itaxotoolscalculatedistances 0.1.1

Calculate Distances




Calculate distances between DNA sequences. Leverages Rust for faster computation.
Originally part of TaxI2.
Installation
calculate_distances is available on PyPI. You can install it through pip:
pip install itaxotools-calculate-distances

Usage
Import the distance calculation functions, each of which take two string arguments:
from itaxotools import calculate_distances as calc

x = "ACGT"
y = "AN-A"

calc.seq_distances_p(x, y) # 0.5
calc.seq_distances_p_gaps(x, y) # 0.66
calc.seq_distances_jukes_cantor(x, y) # 0.82
calc.seq_distances_kimura2p(x, y) # inf

Unit tests
Only basic tests included. More extensive unit testing is currently done as part of TaxI2.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

Share

• Share on Facebook
• Share on Twitter