Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e., species. Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a wellknown problem in computational biology. We propose a novel approach to tackle this problem, mainly to transform a col...

Trees employ impulses of electrical activity to coordinate actions their bodies and long-distance communication. There are indications that the vascular system might act as a network pathways for traveling impulses. A question arises about correlation interplay between molecular (microscopic) level macroscopic observable behavior (the impulses), individual trees component larger living ecosyste...

Abstract. The energy of a molecular graph is a popular parameter that is defined as the sum of the absolute values of a graph’s eigenvalues. It is well known that the energy is related to the matching polynomial and thus also to the Hosoya index via a certain Coulson integral. Trees minimizing the energy under various additional conditions have been determined in the past, e.g., trees with a gi...

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to...

were nonstationary at first positions for the ingroup at P = 0.01 using the chi-square test in PAUP*. The chi-square test in PAUP∗ appears to do a good job of identifying the worst offenders and although crude, is effective for a large data set when analyzing individual genes. We certainly anticipate that as more refined tests of stationarity are implemented (e.g., Foster, 2004), discrimination...

SUMMARY Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database. AVAILABILITY Phyutility, including source code, documentation, examples...