snp-sites binary package in Ubuntu Trusty amd64

 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.

Source package