articleVirus EvolutionJan 1, 2016GOLD OA

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

ARAndrew RambautTTTommy Tsan‐Yuk LamLMLuiz Max CarvalhoOGOliver G. Pybus

Centre for Immunity, Infection and Evolution · Institut de Biologia Evolutiva · +3 more institutions

PubMed
Indexed incrossrefdoajpubmed

Abstract

Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression…

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Topics & keywords

Topics
Keywords
  • Tempest
  • Divergence (linguistics)
  • Phylogenetic tree
  • Sampling (signal processing)
  • Sequence (biology)
  • Molecular clock
  • Biology
  • Visualization
UN Sustainable Development Goals
  • Good health and well-being
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