With rapid increase of nucleotide and amino acid sequence data, it is required to develop reliable and exible application programs to infer molecular phylogenetic trees. The maximum likelihood method is known to be robust among many methods for reconstruction of molecular phylogenetic trees, however, this method requires extremely high computational cost. Although parallel computation is a good...

To estimate approximate divergence times of species or species groups with molecular data, we have developed a method of constructing a linearized tree under the assumption of a molecular clock. We present two tests of the molecular clock for a given topology: two-cluster test and branch-length test. The two-cluster test examines the hypothesis of the molecular clock for the two lineages create...

We present an approach for extracting molecular events from literature based on a deep parser, using in a query language for parse trees. Detected events range from gene expression to protein localization, and cover a multitude of different entity types, including genes/proteins, binding sites, and locations. Furthermore, our approach is capable of recognizing negation and the speculative chara...

Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates of the relative ages of nodes in a molecular evolutionary tree. Both forms of data are often best characterized as yielding continuous probability distributi...

The paper describes a number of molecular methods used in the past and now to analyze forest tree species. Taking into account the economic importance of forest trees and in view of the timber economy, wood properties and characteristics are essential factors subjected to control, observation and research. Molecular techniques that support traditional selection methods allow for genetic diversi...

Trees can improve air quality, but at the same time, pollution might put them at risk. Plane(Platanus orientalis L) and willow trees (Salix babylonicaL) are important trees in the green space of Tehran. Plane trees in Tehran have experienced early autumn in recent years due to severe air pollution. The present study, investigated some physiological traits of these trees under study to determine...

thrips tabaci lindeman is an extensively distributed pest insect in many areas that affects plants through direct feeding and at the same time, it makes damage as a vector of different viruses. as a basic first step to control pests is authentic identification, but the inability to determine morphological characters of thrips species makes this process very difficult. for creating an identifica...

Minimum spanning trees (MSTs) are frequently used in molecular epidemiology research to estimate relationships among individual strains or isolates. Nevertheless, there are significant caveats to MST algorithms that have been largely ignored in molecular epidemiology studies and that have the potential to confound or alter the interpretation of the results of those analyses. Specifically, (i) p...

The most commonly used measure of evolutionary distance in molecular phylogenetics is the number of nucleotide substitutions per site. However, this number is not necessarily most efficient for reconstructing a phylogenetic tree. In order to evaluate the accuracy of evolutionary distance, D(t), for obtaining the correct tree topology, an accuracy index, A(t), was proposed. This index is defined...