Abstract
BackgroundPhylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are open-source libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them.ResultsIn order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself.ConclusionThe Perl package is available as part of the BioPerl bundle, and can also be downloaded. A web-based application is also available (see availability and requirements). The Perl package includes full documentation of all its features.
Highlights
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer
Phylogenetic networks have been studied over the last years as a richer model of the evolutionary history of sets of organisms than phylogenetic trees, because they take into account mutation events and evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer
This allows us to define a distance on the set of tree-child phylogenetic networks on S: the μ-distance between two given networks N1 and N2 is the symmetric difference of their μ-representations, dμ(N1, N2) = |μ(N1) ∆ μ(N2)|. This defines a true distance, and when N1 and N2 are phylogenetic trees, it coincides with the well-known partition distance [8]. This representation allows us to define an optimal alignment between two tree-child phylogenetic networks on S, say n = |S|
Summary
In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by him or herself
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