A fully resolved consensus between fully resolved phylogenetic trees.
نویسندگان
چکیده
Nowadays, there are many phylogeny reconstruction methods, each with advantages and disadvantages. We explored the advantages of each method, putting together the common parts of trees constructed by several methods, by means of a consensus computation. A number of phylogenetic consensus methods are already known. Unfortunately, there is also a taboo concerning consensus methods, because most biologists see them mainly as comparators and not as phylogenetic tree constructors. We challenged this taboo by defining a consensus method that builds a fully resolved phylogenetic tree based on the most common parts of fully resolved trees in a given collection. We also generated results showing that this consensus is in a way a kind of "median" of the input trees; as such it can be closer to the correct tree in many situations.
منابع مشابه
The transposition distance for phylogenetic trees
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phy...
متن کاملThe mean value of the squared path-difference distance for rooted phylogenetic trees
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the path-difference metric between two fully resolved rooted phylogenetic trees with n leaves, under the uniform distribution. This complements previous work by Steel an...
متن کاملMetaheuristic Approaches for Deriving High Quality Fully Resolved Consensus Trees
The consensus tree problem primarily arises in the domain of phylogenetics and seeks to find for a given collection of trees a single tree best representing it. Such a tree collection is usually obtained by biologists for a specific taxa set either via different phylogenetic inference methods or multiple applications of a nondeterministic procedure. Existing consensus methods often have the dis...
متن کاملThe expected value under the Yule model of the squared path-difference distance
The path-difference metric is one of the oldest and most popular distances for the comparison of phylogenetictrees, but its statistical properties are still quite unknown. In this paper we compute the expected valueunder the Yule model of evolution of its square on the space of fully resolved rooted phylogenetic trees withn leaves. This complements previous work by Steel–Penny a...
متن کاملConsistency of Bayesian inference of resolved phylogenetic trees
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a fully resolved evolutionary tree under a wide variety of conditions. This includes the inference of gene trees from aligned sequence data across the entire p...
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:
- Genetics and molecular research : GMR
دوره 5 1 شماره
صفحات -
تاریخ انتشار 2006