A tree metric using structure and length to capture distinct phylogenetic signals
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources (e.g. several genes from the same organisms) and different inference methods. We propose a new metric for robust, quantitative comparison of rooted, labeled trees. It enables clear visualizations of tree space, gives meaningful comparisons between trees, and can detect distinct islands of tree topologies in posterior distributions of trees. This makes it possible to select well-supported summary trees. We demonstrate our approach on Dengue fever phylogenies.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Double-Ended Palindromic Trees: A Linear-Time Data Structure and Its Applications
The palindromic tree (a.k.a. eertree) is a linear-size data structure that provides access to all palindromic substrings of a string. In this paper, we propose a generalized version of eertree, called double-ended eertre…
You Only Need Attention to Traverse Trees
In recent NLP research, a topic of interest is universal sentence encoding, sentence representations that can be used in any supervised task. At the word sequence level, fully attention-based models suffer from two probl…
SentenceHubiness, length, crossings and their relationships in dependency trees
Here tree dependency structures are studied from three different perspectives: their degree variance (hubiness), the mean dependency length and the number of dependency crossings. Bounds that reveal pairwise dependencies…
SentenceBranch length statistics in phylogenetic trees under constant-rate birth-death dynamics
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch le…
An Automatic Machine Translation Evaluation Metric Based on Dependency Parsing Model
Most of the syntax-based metrics obtain the similarity by comparing the sub-structures extracted from the trees of hypothesis and reference. These sub-structures are defined by human and can't express all the information…
Dependency ParsingMachine TranslationSentenceTranslation