snp-sites command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

snp-sites: command not found

or when using sudo you get the following error message

sudo: snp-sites: command not found

Solutions to snp-sites: command not found

How To Fix snp-sites: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu snp-sites is provided by snp-sites package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install snp-sites

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install snp-sites.

sudo apt -y install snp-sites

Or if you have aptitude installed you can use the following command.

sudo aptitude install snp-sites

Summary

In this tutorial we learn how to fix snp-sites command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.