相关论文: Sound Colless-like balance indices for multifurcat…

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…

This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…

Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…

Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

Difference balanced functions from $F_{q^n}^*$ to $F_q$ are closely related to combinatorial designs and naturally define $p$-ary sequences with the ideal two-level autocorrelation. In the literature, all existing such functions are…

There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the…

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

This paper proposes FREEtree, a tree-based method for high dimensional longitudinal data with correlated features. Popular machine learning approaches, like Random Forests, commonly used for variable selection do not perform well when there…

A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…

The index of a Lie algebra $\mathfrak{g}$ is defined by ind $\mathfrak{g}=$ $\min_{f\in \mathfrak{g}^*}\dim(\ker (B_f))$, where $f$ is an element of the linear dual $\mathfrak{g}^*$ and $B_f(x,y)=f([x,y])$ is the associated skew-symmetric…

We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…

Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…

One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…

Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of…

We prove that in both the free and the wired uniform spanning forest (FUSF and WUSF) of any unimodular random rooted network (in particular, of any Cayley graph), it is impossible to distinguish the connected components of the forest from…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…