Metadata-Version: 2.4
Name: alnPairDist
Version: 1.0.5
Summary: alnPairDist: A tool for calculating pairwise similarity of taxa in a multiple sequence alignment
Author-email: Chrispin Chaguza <chrispin.chaguza@gmail.com>
Maintainer-email: Chrispin Chaguza <chrispin.chaguza@gmail.com>
License: MIT License
        
        Copyright (c) 2026 Chrispin Chaguza
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
Project-URL: Homepage, https://github.com/ChrispinChaguza/alnPairDist/
Project-URL: Repository, https://github.com/ChrispinChaguza/alnPairDist.git
Project-URL: Issues, https://github.com/ChrispinChaguza/alnPairDist/issues
Project-URL: Documentation, https://github.com/ChrispinChaguza/alnPairDist/
Project-URL: Website, https://github.com/ChrispinChaguza/alnPairDist
Keywords: Sequence alignment,Pairwise distance,Nucleotides
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: setuptools
Requires-Dist: toml
Requires-Dist: biopython
Dynamic: license-file

# alnPairDist: A tool for calculating pairwise similarity of taxa in a multiple sequence alignment

## Getting the alnPairDist source code
```
git clone https://github.com/ChrispinChaguza/alnPairDist.git
```

## Setup alnPairDist software on a local machine

### Installing alnPairDist using Pip

The easist way to install the latest version of alnPairDist is using Pip
```
pip install alnPairDist
```

Here is a command to install a specific version of ViralLC using Pip
```
pip install alnPairDist=={INSERT VERSION HERE}
```

### Installing ViralLC using Conda

Installation using Conda (upcoming!).
```
conda install -c conda-forge alnPairDist
```
```
conda install -c bioconda alnPairDist
```

### Installing ViralLC directly from Github

First, download alnPairDist from GitHub and then manually setup the environment for the package 

```
git clone https://github.com/ChrispinChaguza/alnPairDist.git
cd alnPairDist
```

Second, manually install the required package dependencies 

```
conda install -c conda-forge python=3.14.2 -y
conda install -c conda-forge biopython=1.86 -y
```
```
pip install build
```


Follow the instructions below to build and install alnPairDist
```
python -m build 
pip install --force-reinstall dist/{INSERT THE COMPILED SOFTWARE VERSION} 
```

## Basic usage


The simplest way to run alnPairDist is to provide a multiple sequence alignment in FASTA format
```
alnPairDist --aln input.fasta --out report.tsv
```
```
alnPairDist -a input.fasta -o report.tsv 
```

Specify the "--threads" or "-t" option to use more threads
```
alnPairDist --aln input.fasta --out report.tsv --threads 10
```
```
alnPairDist -a input.fasta -o report.tsv -t 10
```

To suppress the output on the terminal
```
alnPairDist --aln input.fasta --out report.tsv --threads 10 --quiet
```
```
alnPairDist --aln input.fasta --out report.tsv --threads 10 -q
```
### Example dataset (Rotavirus A)

Calculating pairwise distances between sequences using the *example.aln* alignment file in the *example* directory
```
alnPairDist --aln example.aln --out report.tsv --threads 10
```

### Software version

Run the command below to show the software version
```
alnPairDist --version
```
``` 
alnPairDist -v
```

## Cite
Chrispin Chaguza, alnPairDist, https://github.com/ChrispinChaguza/alnPairDist.git
