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Volume 5, Issue 1

HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny Open Access

Abstract

A homoplasy is a nucleotide identity resulting from a process other than inheritance from a common ancestor. Importantly, by distorting the ancestral relationships between nucleotide sequences, homoplasies can change the structure of the phylogeny. Homoplasies can emerge naturally, especially under high selection pressures and/or high mutation rates, or be created during the generation and processing of sequencing data. Identification of homoplasies is critical, both to understand their influence on the analyses of phylogenetic data and to allow an investigation into how they arose. Here we present HomoplasyFinder, a java application that can be used as a stand-a-lone tool or within the statistical programming environment R. Within R and Java, HomoplasyFinder is shown to be able to automatically, and quickly, identify any homoplasies present in simulated and real phylogenetic data. HomoplasyFinder can easily be incorporated into existing analysis pipelines, either within or outside of R, allowing the user to quickly identify homoplasies to inform downstream analyses and interpretation.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): convergence , homoplasy , HomoplasyFinder , Java , phylogenetic and R package
© 2019 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2019-01-21
2024-04-19
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HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
M Gen 5, e000245 (2019); https://doi.org/10.1099/mgen.0.000245
/content/journal/mgen/10.1099/mgen.0.000245
/content/journal/mgen/10.1099/mgen.0.000245
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