Sequence Variation Analysis,Maps and Phylogeny

SVAMP is standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples. SVAMP has some interesting features like phylogeography,allele frequency map and principal coordinate analysis.SVAMP takes VCF files (variant call format) as input. Metainformation on samples are simple tab delimited text files.In addition SVAMP also reads annotation files in GFF format and reference sequences in FASTA format. For more information on SVAMP please see the publication SVAMP: sequence variation analysis, maps and phylogeny.

The software was developed at the Pathogen Genomics Laboratory (PI: Arnab Pain) in KAUST.

Screenshot from SVAMP software shows
A) Variation across 63 MRSA isolates from 15 countries.
B) Allele frequency map of a variation site in the genome
C) PCoA plot colour-coded by geographical region of isolation.
D) Circular phylogeny color-coded by geographical region of isolation.


  1. Download the latest binaries (v 2.10) for your platform from DOWNLOADS section

  2. Download the MRSA dataset

  3. Unzip the software binary and dataset to a location where the user has permission to create files. Please note that SVAMP creates all temporary files in the same working directory where binary resides.

  4. double click on the SVAMP executable to open the application.

  5. File->load open the mrsa_science_bundle and TW20_full.fasta,TW20_full.gff,tw20_4310.vcf,tw20.db and click load.

  6. Tools->Tree,Tools->PCOA, Tools->Allele Map to visualise the Tree,PCOA plot and allele frequence map.

  7. click on the checkbox adjacent to GCdensity,Relative variant density,Fst and Tajima's D tracks to enable the respective graphs.

Download software and sample dataset (latest version is now 2.10 released on 18th March 2014)


  • PCOA
  • Phylogenetic tree : circular

  • Phylogenetic tree : non-circular, with selected regions
  • Graphs

  • Isolate geographical distribution

  • Map of Allele Frequency Distribution


For download and installation instructions and features see SVAMP manual


Please contact Raeece Naeem or Lailatul Hidayah for any questions and comments about SVAMP.