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.
2 maintainers
Release files for itaxotools-calculate-distances 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| itaxotools_calculate_distances-0.1.1.tar.gz | 26.6 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| itaxotools_calculate_distances-0.1.1-cp37-abi3-win_amd64.whl | CPython 3.7 | abi3 | Windows x86-64 | Details |
| itaxotools_calculate_distances-0.1.1-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.7 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| itaxotools_calculate_distances-0.1.1-cp37-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl | CPython 3.7 | abi3 | macOS 10.12+ universal2 (ARM64, x86-64), macOS 11.0+ ARM64, macOS 10.12+ x86-64 | Details |
Total release size: 2.1 MB
Release files / itaxotools_calculate_distances-0.1.1.tar.gz
| Download URL | itaxotools_calculate_distances-0.1.1.tar.gz |
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| Size | 26.6 kB |
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Release files / itaxotools_calculate_distances-0.1.1-cp37-abi3-win_amd64.whl
| Download URL | itaxotools_calculate_distances-0.1.1-cp37-abi3-win_amd64.whl |
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| Size | 196.1 kB |
| Tags | CPython 3.7 Windows x86-64 abi3 |
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Release files / itaxotools_calculate_distances-0.1.1-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | itaxotools_calculate_distances-0.1.1-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 1.2 MB |
| Tags | CPython 3.7 Linux glibc 2.17+ x86-64 abi3 |
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Release files / itaxotools_calculate_distances-0.1.1-cp37-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl
| Download URL | itaxotools_calculate_distances-0.1.1-cp37-abi3-macosx_10_12_x86_64.macosx_11_0_arm64.macosx_10_12_universal2.whl |
|---|---|
| Size | 668.0 kB |
| Tags | CPython 3.7 abi3 macOS 10.12+ universal2 (ARM64, x86-64) macOS 10.12+ x86-64 macOS 11.0+ ARM64 |
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