On the quirks of maximum parsimony and likelihood on phylogenetic networks
نویسندگان
چکیده
منابع مشابه
Surprising properties of Maximum Parsimony on phylogenetic networks
Phylogenetic inference aims at reconstructing the evolutionary relationships of different species given some data (e.g. DNA, RNA or proteins). Traditionally, the relationships between species were assumed to be treelike, so the most frequently used phylogenetic inference methods like Maximum Parsimony were originally introduced to reconstruct phylogenetic trees. However, it has been well-known ...
متن کاملMaximum likelihood of phylogenetic networks
MOTIVATION Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative. RESULTS In this art...
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Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as Maximum Parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two different definitions of Maximum Parsimony ...
متن کاملOn the Maximum Parsimony distance between phylogenetic trees
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the chara...
متن کاملParsimony accelerated Maximum Likelihood searches
Phylogenetic 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 parsimony as an initial estimator for ML. ...
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ژورنال
عنوان ژورنال: Journal of Theoretical Biology
سال: 2017
ISSN: 0022-5193
DOI: 10.1016/j.jtbi.2017.01.013