Approximating Subtree Distances Between Phylogenies
نویسندگان
چکیده
We give a 5-approximation algorithm to the rooted Subtree-Prune-and-Regraft (rSPR) distance between two phylogenies, which was recently shown to be NP-complete. This paper presents the first approximation result for this important tree distance. The algorithm follows a standard format for tree distances. The novel ideas are in the analysis. In the analysis, the cost of the algorithm uses a "cascading" scheme that accounts for possible wrong moves. This accounting is missing from previous analysis of tree distance approximation algorithms. Further, we show how all algorithms of this type can be implemented in linear time and give experimental results.
منابع مشابه
Approximating the Maximum Isomorphic Agreement Subtree Is Hard
The Maximum Isomorphic Agreement Subtree (MIT) problem is one of the simplest versions of the Maximum Interval Weight Agreement Subtree method (MIWT) which is used to compare phylogenies. More precisely MIT allows to provide a subset of the species such that the exact distances between species in such subset are preserved among all evolutionary trees considered. In this paper, the approximation...
متن کاملImproved Phylogeny Comparisons: Non-shared Edges, Nearest Neighbor Interchanges, and Subtree Transfers
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest neighbor interchange (NNI) distance. In this paper, we give the rst subquadratic-time algorithm for nding the non-shared edges, which are then used to speed up the ...
متن کاملOn the Linear-cost Subtree-transfer Distance between Phylogenetic Trees (revised Version of Dimacs Technical Report 97-18) 1
Di erent phylogenetic trees for the same group of species are often produced either by procedures that use diverse optimality criteria [16] or from di erent genes [12] in the study of molecular evolution. Comparing these trees to nd their similarities and dissimilarities (i.e. distance) is thus an important issue in computational molecular biology. Several distance metrics including the nearest...
متن کاملA Unifying View on Approximation and FPT of Agreement Forests
We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linearor O(n logn)-time 3-approximation and improved fixed-parameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridizat...
متن کاملA Unifying View on Approximation and FPT of Agreement Forests (Extended Abstract⋆)
We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linearor O(n log n)-time 3-approximation and improved fixed-parameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridiza...
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:
- Journal of computational biology : a journal of computational molecular cell biology
دوره 13 8 شماره
صفحات -
تاریخ انتشار 2006