Background and Aims: The Inclusion Body Hepatitis disease (IBH) is one of the prevalent illnesses in our country these days and reported from different regions of Iran. In addition to its fatality, the importance of this disease is disturbing the vaccination program in poultry, especially broiler chickens, against other diseases like infectious bursal disease (IBD) and Newcastle disease (ND). T...

Phylogenetic trees are commonly reconstructed based on hard optimization problems such as maximum parsimony (MP) and maximum likelihood (ML). Conventional MP heuristics for producing phylogenetic trees produce good solutions within reasonable time on small datasets (up to a few thousand sequences), while ML heuristics are limited to smaller datasets (up to a few hundred sequences). However, sin...

A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the p...

Model intercomparison exercises have identified radionuclide transfer predictions as the greatest source of uncertainty in biota dose assessments. One wildlife group for which few transfer data exist is reptiles, Given that reptiles are an important, and often protected, component of many ecosystems and that assessments of radiation impact on ecosystems are becoming increasingly necessary due t...

Inferring phylogenetic trees from sequence or morphological characters is computationally intensive, and requires the use of heuristics. The search space and fitness landscape of treespace for even modest datasets is large and multi-modal. Traditional computational approaches typically involve hill-climbing using intra-tree branch-swapping techniques such as subtree pruning and re-grafting (SPR...

FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment bl...

The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements (‘motifs’) based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we ...

The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequences of these rearrangements. However, even simple models lead to NP-hard problems, particularly in the area of phylogenetic analysis. Current a...

BACKGROUND Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogen...

Until recently, rigorously reconstructing the many hybrid speciation events in plants has not been practical because of the limited number of molecular markers available for plant phylogenetic reconstruction and the lack of good, biologically based methods for inferring reticulation (network) events. This situation should change rapidly with the development of multiple nuclear markers for phylo...