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Local Search for the Maximum Parsimony Problem
, 2005 Four local search algorithms are investigated for the phylogenetic tree reconstruction problem under the Maximum Parsimony criterion. A new subtree swapping neighborhood is introduced and studied in combination with an effective array-based tree representation.
Goëffon, Adrien +2 more
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A Subdivision Approach to Maximum Parsimony
Annals of Combinatorics, 2008Determining an optimal phylogenetic tree using maximum parsimony, also referred to as the Steiner tree problem in phylogenetics, is NP hard. Here we provide a new formulation for this problem which leads to an analytical and linear time solution when the dimensionality (sequence length, or number of characters) is at most two.
David Bryant
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Maximum Parsimony for Tree Mixtures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to processes such as gene duplication and lineage sorting, it is important to better understand how ...
Stefan Grünewald, Vincent Moulton
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Parsimony accelerated Maximum Likelihood searches
International Journal of Computational Biology and Drug Design, 2008Phylogenetic search is a key tool used in a variety of biological research endeavours. However, this search problem is known to be computationally difficult, due to the astronomically large search space, making the use of heuristic methods necessary. The performance of heuristic methods for finding Maximum Likelihood (ML) trees can be improved by using
Kenneth Sundberg +4 more
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Characterizing Local Optima for Maximum Parsimony
Bulletin of Mathematical Biology, 2016Finding the best phylogenetic tree under the maximum parsimony optimality criterion is computationally difficult. We quantify the occurrence of such optima for well-behaved sets of data. When nearest neighbor interchange operations are used, multiple local optima can occur even for "perfect" sequence data, which results in hill-climbing searches that ...
Ellen Urheim +2 more
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A probabilistic version of Sankoff’s maximum parsimony algorithm
Journal of Bioinformatics and Computational Biology, 2020The number of genes belonging to a multi-gene family usually varies substantially over their evolutionary history as a consequence of gene duplications and losses. A first step toward analyzing these histories in detail is the inference of the changes in copy number that take place along the individual edges of the underlying phylogenetic tree.
Gábor Balogh +3 more
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Maximum Parsimony Method for Phylogenetic Prediction
Cold Spring Harbor Protocols, 2008INTRODUCTIONMaximum parsimony predicts the evolutionary tree or trees that minimize the number of steps required to generate the observed variation in the sequences from common ancestral sequences. For this reason, the method is also sometimes referred to as the minimum evolution method.
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Evolution of cytochromec investigated by the maximum parsimony method
Journal of Molecular Evolution, 1981Rates of evolution for cytochrome c over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochrome c molecule.
M L, Baba +3 more
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Maximum Parsimony, Substitution Model, and Probability Phylogenetic Trees
Journal of Computational Biology, 2011The problem of inferring phylogenies (phylogenetic trees) is one of the main problems in computational biology. There are three main methods for inferring phylogenies-Maximum Parsimony (MP), Distance Matrix (DM) and Maximum Likelihood (ML), of which the MP method is the most well-studied and popular method.
Jia F. Weng +2 more
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A tabu search algorithm for maximum parsimony phylogeny inference
European Journal of Operational Research, 2007zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Yu-Min Lin +2 more
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