Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines...

The field of bioinformatics is witnessing a rapid and overwhelming accumulation of molecular sequence data, predominantly driven by novel wet-lab sequencing techniques. This trend poses scalability challenges for tool developers. In the field of phylogenetic inference (reconstruction of evolutionary trees from molecular sequence data), scalability is becoming an increasingly important issue for...

This work deals with symbolic mathematical solutions to maximum likelihood on small phylogenetic trees. Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. In this work, we give general analytic solutions for a family of trees with four taxa, two state characters, under a molecular...

The cultivated apple (Malus domestica) is one of the most important fruit crops cultivated in different regions of the world including Iran. For production and breeding of high quality apple, the knowledge of genetic diversity of the cultivated apples  is  necessary. Therefore we studied genetic diversity of 25 genotypes by using ISSR molecular markers. In present study, ten ISSR primers produc...

theplant pathogenic phytophthora drechsleri is morphologically similar to some other non-papillate phytophthora spp., especially p. melonis, and it is difficult to discriminate these convergent taxa. it seems that the iranian putative p. drechsleri isolates from different cucurbit species have been generally misidentified and their characteristics do not match with p. drechsleri. in order to co...

MOTIVATION Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments. In this work, the ...

To determine the mechanism of molecular evolution, molecular biologists need to carry out reconciliation work. In reconciliation work, they compare the relation between two heterogeneous phylogenetic trees and the relation between a phylogenetic tree and a taxonomic tree are compared. Phylogenetic trees and taxonomic trees are referred to as ordered trees and a reconciliation graph is construct...

and expresses complexity at different levels of molecular organization (CaetanoAnollés et al., 2009). At high levels, evolutionary change occurs at extraordinary slow pace. A new protein fold can take millions of years to materialize in sequence space while new sequences develop in less than microseconds. Structural cores are generally orders of magnitude more conserved than sequences. Conseque...

All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high conf...