Biomedical subjects

Christian N S Pedersen

Publications and source records attributed to Christian N S Pedersen.

8 recordsLinked to original sources

PubMed2006

Fast calculation of the quartet distance between trees of arbitrary degrees.

BACKGROUND: A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets - sub-trees induced by four leaves - that differs between the trees. Mostly, these algorithms are restricted to work on binary trees, but recently we have developed algorithms that work on trees of arbitrary degree. RESULTS: We present a fast algorithm for computing the quartet distance between trees of arbitrary degree. Given input trees T and T', the algorithm runs in time O(n + /V/./V'/ min{id, id'}) and space O(n + /V/./V'/), where n is the number of leaves in the two trees, V and V are the non-leaf nodes in T and T', respectively, and id and id' are the maximal number of non-leaf nodes adjacent to a non-leaf node in T and T', respectively. The fastest algorithms previously published for arbitrary degree trees run in O(n3) (independent of the degree of the tree) and O(/V/./V'/.id.id'), respectively. We experimentally compare the algorithm with existing algorithms for computing the quartet distance for general trees. CONCLUSION: We present a new algorithm for computing the quartet distance between two trees of arbitrary degree. The new algorithm improves the asymptotic running time for computing the quartet distance, compared to previous methods, and experimental results indicate that the new method also performs significantly better in practice.

Journal Article↗

PubMed2006

GeneRecon--a coalescent based tool for fine-scale association mapping.

UNLABELLED: GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and microsatellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis-Hastings sampling in the state space of genealogies. Input format, search strategy and the sampled statistics can be configured through the Guile Scheme programming language embedded in GeneRecon, making GeneRecon highly configurable. AVAILABILITY: The source code for GeneRecon, written in C++ and Scheme, is available under the GNU General Public License (GPL) at http://www.birc.au.dk/~mailund/GeneRecon CONTACT: mailund@birc.au.dk.

Algorithms↗

PubMed2006

Recrafting the neighbor-joining method.

BACKGROUND: The neighbor-joining method by Saitou and Nei is a widely used method for constructing phylogenetic trees. The formulation of the method gives rise to a canonical Theta(n3) algorithm upon which all existing implementations are based. RESULTS: In this paper we present techniques for speeding up the canonical neighbor-joining method. Our algorithms construct the same phylogenetic trees as the canonical neighbor-joining method. The best-case running time of our algorithms are O(n2) but the worst-case remains O(n3). We empirically evaluate the performance of our algoritms on distance matrices obtained from the Pfam collection of alignments. The experiments indicate that the running time of our algorithms evolve as Theta(n2) on the examined instance collection. We also compare the running time with that of the QuickTree tool, a widely used efficient implementation of the canonical neighbor-joining method. CONCLUSION: The experiments show that our algorithms also yield a significant speed-up, already for medium sized instances.

Algorithms↗

PubMed2005

CoaSim: a flexible environment for simulating genetic data under coalescent models.

BACKGROUND: Coalescent simulations are playing a large role in interpreting large scale intra-specific sequence or polymorphism surveys and for planning and evaluating association studies. Coalescent simulations of data sets under different models can be compared to the actual data to test the importance of different evolutionary factors and thus get insight into these. RESULTS: We have created the CoaSim application as a flexible environment for Monte Carlo simulation of various types of genetic data under equilibrium and non-equilibrium coalescent processes for a variety of applications. Interaction with the tool is through the Guile version of the Scheme scripting language. Scheme scripts for many standard and advanced applications are provided and these can easily be modified by the user for a much wider range of applications. A graphical user interface with less functionality and flexibility is also included. It is primarily intended as an exploratory and educational tool CONCLUSION: CoaSim is a powerful tool because of its flexibility and ease of use. This is illustrated through very varied uses of the application, e.g. evaluation of association mapping methods, parametric bootstrapping, and design and choice of markers for specific questions.

Case-Control Studies↗

PubMed2004

RBT--a tool for building refined Buneman trees.

SUMMARY: We have developed a tool implementing an efficient algorithm for refined Buneman tree reconstruction. The algorithm--which has the same complexity as the neighbour-joining method and the (plain) Buneman tree construction--enables refined Buneman tree reconstruction on large taxa sets. AVAILABILITY: The source code for RBT, written in Java, is available under the GNU Public License (GPL) at http://www.birc.dk/Software/RBT CONTACT: besen@daimi.au.dk.

Algorithms↗

PubMed2004

QuickJoin--fast neighbour-joining tree reconstruction.

We have built a tool for fast construction of very large phylogenetic trees. The tool uses heuristics for speeding up the neighbour-joining algorithm-while still constructing the same tree as the original neighbour-joining algorithm-making it possible to construct trees for 8000 species in <10 min on a single desktop PC. In comparison, the same task takes more than 30 min using the QuickTree neighbour-joining implementation.

Algorithms↗

PubMed2004

QDist--quartet distance between evolutionary trees.

SUMMARY: QDist is a program for computing the quartet distance between two unrooted trees, i.e. the number of quartet topology differences between the trees, where a quartet topology is the topological subtree induced by four species. The program is based on an algorithm with running time O(n log2 n), which makes it practical to compare large trees. Available under GNU license. AVAILABILITY: http://www.birc.dk/Software/QDist

Algorithms↗

PubMed2003

Recursions for statistical multiple alignment.

Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne-Kishino-Felsenstein model for a fixed set of parameters. The algorithms are based on a Markov chain generating sequences and their alignment at nodes in a tree. Depending on whether the complete realization of this Markov chain is decomposed into the first transition and the rest of the realization or the last transition and the first part of the realization, two kinds of recursions are obtained that are computationally similar but probabilistically different. The running time of the algorithms is O(Pi id=1 Li), where Li is the length of the ith observed sequences and d is the number of sequences. An alternative recursion is also formulated that uses only a Markov chain involving the inner nodes of a tree.

Algorithms↗