Walks in phylogenetic treespace
نویسندگان
چکیده
We prove that the spaces of unrooted phylogenetic trees are Hamiltonian for two popular search metrics: Subtree Prune and Regraft (SPR) and Tree Bisection and Reconnection (TBR). Further, we make progress on two conjectures of Bryant on searching phylogenetic treespace: treespace under the Nearest Neighbor Interchange (NNI) metric has a 2-walk, and there exists SPR neighborhoods without complete NNI walks.
منابع مشابه
treespace: Statistical exploration of landscapes of phylogenetic trees
The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as rele...
متن کاملVisualizing Restricted Landscapes of Phylogenetic Trees
We are designing tools to visualize very large sets of phylogenetic trees. Our tools give a three dimesional representation of treespace, with two dimensions representing the clustering of trees under multidimensional scaling, and the third dimension (the “height”) the score of the tree (i.e. parsimony or maximum likelihood score). The user can rotate the resulting distribution to get a sense o...
متن کاملMean and Variance of Phylogenetic Trees
Abstract.— We describe the use of the Fréchet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, despite its stickiness property, and that the Fréchet variance is faster and more precise than commonly used variance measures. These mean and va...
متن کاملA combinatorial method for connecting BHV spaces representing different numbers of taxa
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique to BHV tree space is well known to be computable in polynomial time, which makes it a potentially powerful tool for optimization problems in phylogenetics an...
متن کاملA Survey of Evolutionary Crossover Operators as Applied to Phylogenetic Inferencing
Inferring phylogenetic trees from sequence or morphological characters is computationally intensive, and requires the use of heuristics. The search space and fitness landscape of treespace for even modest datasets is large and multi-modal. Traditional computational approaches typically involve hill-climbing using intra-tree branch-swapping techniques such as subtree pruning and re-grafting (SPR...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Inf. Process. Lett.
دوره 111 شماره
صفحات -
تاریخ انتشار 2011