{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T19:23:09Z","timestamp":1776885789156,"version":"3.51.2"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":949,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima\u2019s D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents.<\/jats:p>\n               <jats:p>Availability and implementation: The Qt\/C++ software code, binaries, user manual and example datasets are available at http:\/\/cbrc.kaust.edu.sa\/svamp<\/jats:p>\n               <jats:p>Contact: \u00a0arnab.pain@kaust.edu.sa or arnab.pain@cantab.net<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu176","type":"journal-article","created":{"date-parts":[[2014,4,4]],"date-time":"2014-04-04T01:54:59Z","timestamp":1396576499000},"page":"2227-2229","source":"Crossref","is-referenced-by-count":4,"title":["SVAMP: sequence variation analysis, maps and phylogeny"],"prefix":"10.1093","volume":"30","author":[{"given":"Raeece","family":"Naeem","sequence":"first","affiliation":[{"name":"1 Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and 2 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lailatul","family":"Hidayah","sequence":"additional","affiliation":[{"name":"1 Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and 2 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark D.","family":"Preston","sequence":"additional","affiliation":[{"name":"1 Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and 2 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[{"name":"1 Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and 2 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arnab","family":"Pain","sequence":"additional","affiliation":[{"name":"1 Pathogen Genomics Laboratory, Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia and 2 Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,4,3]]},"reference":[{"key":"2023012711522205500_btu176-B1","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1504\/IJCBDD.2013.052204","article-title":"PolyLens: software for map-based visualisation and analysis of genome-scale polymorphism data","volume":"6","author":"Berry","year":"2013","journal-title":"Int.l J. 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