200 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
An Algebraic View of the Relation between Largest Common Subtrees and Smallest Common Supertrees
The relationship between two important problems in tree pattern matching, the
largest common subtree and the smallest common supertree problems, is
established by means of simple constructions, which allow one to obtain a
largest common subtree of two trees from a smallest common supertree of them,
and vice versa. These constructions are the same for isomorphic, homeomorphic,
topological, and minor embeddings, they take only time linear in the size of
the trees, and they turn out to have a clear algebraic meaning.Comment: 32 page
Redundancy and subsumption in high-level replacement systems
System verification in the broadest sense deals with those semantic
properties that can be decided or deduced by analyzing a syntactical
description of the system. Hence, one may consider the notions of
redundancy and subsumption in this context as they are known from the
area of rule-based systems. A rule is redundant if it can be removed
without affecting the semantics of the system; it is subsumed by
another rule if each application of the former one can be replaced by
an application of the latter one with the same effect. In this paper,
redundancy and subsumption are carried over from rule-based systems to
high-level replacement systems, which in turn generalize graph and
hypergraph grammars. The main results presented in this paper are a
characterization of subsumption and a sufficient condition for
redundancy, which involves composite productions.Postprint (published version
On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa
Compatibility of phylogenetic trees is the most important concept underlying
widely-used methods for assessing the agreement of different phylogenetic trees
with overlapping taxa and combining them into common supertrees to reveal the
tree of life. The notion of ancestral compatibility of phylogenetic trees with
nested taxa was introduced by Semple et al in 2004. In this paper we analyze in
detail the meaning of this compatibility from the points of view of the local
structure of the trees, of the existence of embeddings into a common supertree,
and of the joint properties of their cluster representations. Our analysis
leads to a very simple polynomial-time algorithm for testing this
compatibility, which we have implemented and is freely available for download
from the BioPerl collection of Perl modules for computational biology.Comment: Submitte
Extended Newick: it is time for a standard representation of phylogenetic networks
<p>Abstract</p> <p>Background</p> <p>Phylogenetic trees resulting from molecular phylogenetic analysis are available in Newick format from specialized databases but when it comes to phylogenetic networks, which provide an explicit representation of reticulate evolutionary events such as recombination, hybridization or lateral gene transfer, the lack of a standard format for their representation has hindered the publication of explicit phylogenetic networks in the specialized literature and their incorporation in specialized databases. Two different proposals to represent phylogenetic networks exist: as a single Newick string (where each hybrid node is splitted once for each parent) or as a set of Newick strings (one for each hybrid node plus another one for the phylogenetic network).</p> <p>Results</p> <p>The standard we advocate as extended Newick format describes a whole phylogenetic network with <it>k </it>hybrid nodes as a single Newick string with <it>k </it>repeated nodes, and this representation is unique once the phylogenetic network is drawn or the ordering among children nodes is fixed. The extended Newick format facilitates phylogenetic data sharing and exchange, and also allows for the practical use of phylogenetic networks in computer programs and scripts. This standard has been recently agreed upon by a number of computational biologists, is already supported by several phylogenetic tools, and avoids the different drawbacks of using an a priori unknown number of Newick strings without any additional mark-up to represent a phylogenetic network.</p> <p>Conclusion</p> <p>The adoption of the extended Newick format as a standard for the representation of phylogenetic network is an important step towards the publication of explicit phylogenetic networks in peer-reviewed journals and their incorporation in a future database of published phylogenetic networks.</p
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