Calculate distances between DNA sequences
Project description
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.
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