A Perl Package and an Alignment Tool for Phylogenetic Networks

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Abstract
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. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, and there are no open-source libraries either. 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 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 herself. The Perl package has been accepted as part of the BioPerl bundle. It can be downloaded from http://dmi.uib.es/~gcardona/BioInfo/Bio-PhyloNetwork.tgz. The web-based application is available at http://dmi.uib.es/~gcardona/BioInfo/. The Perl package includes full documentation of all its features.
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