Open AccessHomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
Author(s) -
Joseph Crispell,
Daniel Balaz,
Stephen V. Gordon
Publication year - 2019
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000245
Subject(s) - phylogenetic tree , computer science , inheritance (genetic algorithm) , identification (biology) , process (computing) , data mining , biology , programming language , genetics , ecology , gene
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.