itaxotools-calculate-distances 0.1.1

Calculate distances between DNA sequences

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.