2,579 research outputs found
A Perl Package and an Alignment Tool for Phylogenetic Networks
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.Comment: 5 page
The expected value under the Yule model of the squared path-difference distance
The path-difference metric is one of the oldest and most popular distances
for the comparison of phylogenetic trees, but its statistical properties are
still quite unknown. In this paper we compute the expected value under the Yule
model of evolution of its square on the space of fully resolved rooted
phylogenetic trees with n leaves. This complements previous work by Steel-Penny
and Mir-Rossell\'o, who computed this mean value for fully resolved unrooted
and rooted phylogenetic trees, respectively, under the uniform distribution.Comment: 10 pages, extended version of a paper submitted to Applied
Mathematics Lette
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