How To Install snp-sites on Kali Linux
Introduction
In this tutorial we learn how to install snp-sites on Kali Linux.
What is snp-sites
snp-sites is:
This program finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip).
The software has been developed at the Wellcome Trust Sanger Institute.
A Single Nucleotide - polymorphism (SNP, pronounced snip; plural snips) is a DNA sequence variation occurring when a Single Nucleotide ?? A, T, C or G ?? in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes. For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case there are two alleles. Almost all common SNPs have only two alleles.
There are three methods to install snp-sites on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install snp-sites Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install snp-sites using apt-get by running the following command:
sudo apt-get -y install snp-sitesInstall snp-sites Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install snp-sites using apt by running the following command:
sudo apt -y install snp-sitesInstall snp-sites Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install snp-sites using aptitude by running the following command:
sudo aptitude -y install snp-sitesHow To Uninstall snp-sites on Kali Linux
To uninstall only the snp-sites package we can use the following command:
sudo apt-get remove snp-sitesUninstall snp-sites And Its Dependencies
To uninstall snp-sites and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove snp-sitesRemove snp-sites Configurations and Data
To remove snp-sites configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge snp-sitesRemove snp-sites configuration, data, and all of its dependencies
We can use the following command to remove snp-sites configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snp-sitesDependencies
snp-sites have the following dependencies:
References
Summary
In this tutorial we learn how to install snp-sites package on Kali Linux using different package management tools: apt, apt-get and aptitude.