alnPairDist 1.0.3

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

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