Discover Community Create You

Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Article

SVAMP: sequence variation analysis, maps and phylogeny.

Bioinformatics (Oxford, England) - 1 Aug 2014

Naeem Raeece, Hidayah Lailatul, Preston Mark D, Clark Taane G, Pain Arnab

Abstract excerpt

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's D metric, single nucleotide...

Read the complete abstract on PubMed

Topics

Share this publication in a Topic to start or enrich a Post.

Share to Disease Outbreaks
Share to Genomics
Share to High-Throughput Nucleotide Sequencing

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Share to Malaria, Falciparum

Share to Methicillin-Resistant Staphylococcus aureus

Share to Plasmodium falciparum

Share to Software

Share to Staphylococcal Infections

Source

Open in PubMed Open full text

Identifiers

PMID: 24700318
DOI: 10.1093/bioinformatics/btu176
PMCID: PMC4103593

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-08.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

SVAMP: sequence variation analysis, maps and phylogeny.PMID 24700318Read ↗

VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data.Semantic proximity Read ↗

vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisationSemantic proximity Read ↗

vSNP: a SNP pipeline for the generation of transparent SNP matrices and phylogenetic trees from whole genome sequencing data sets.Semantic proximity Read ↗

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.Semantic proximity Read ↗

Staphylococcus aureus viewed from the perspective of 40,000+ genomesSemantic proximity Read ↗

PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.Semantic proximity Read ↗

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.Semantic proximity Read ↗

Publication-ready single nucleotide polymorphism visualization with snipit.Semantic proximity Read ↗

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations.Semantic proximity Read ↗

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.Semantic proximity Read ↗

VIVID: a web application for variant interpretation and visualisation in multidimensional analysesSemantic proximity Read ↗

<i>Staphylococcus aureus</i> viewed from the perspective of 40,000+ genomesSemantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.