Several metrics have been developed for estimating phylogenetic signal in comparative data. These may be important both in guiding future studies on correlated evolution and for inferring broad-scale evolutionary and ecological processes (e.g., phylogenetic niche conservatism). Notwithstanding, the validity of some of these metrics is under debate, especially after the development of more sophi...

As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be over...

in order to develop a method for detecting and identification of theileria annulata, the specific primers from the major merozoite-piroplasm surface antigen sequence of theileria (tams1) were used to detect the t. annulata by nested-pcr technique. the assay provides a valuable tool for the identification of theileria annulata directly from clinical samples and enables determination of the infec...

background: computational identification of phylogenetic motifs helps to understand the knowledge about known functional features that includes catalytic site, substrate binding epitopes, and protein-protein interfaces. furthermore, they are strongly conserved among orthologs, indicating their evolutionary importance. the study aimed to analyze five candidate genes involved in type ii diabetic ...

background: newcastle disease virus (ndv) is the causativeagent of the newcastle disease (nd), a highly contagiousdisease in birds that causes significant economic losses to thepoultry industry worldwide. nd is endemic in iran and outbreaksare reported regularly in commercial poultry flocks and differentspecies of birds. objectives:the current study was carried outto characterize ndv based on p...

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in...

Meta-analysis is increasingly used in ecology and evolutionary biology. Yet, in these fields this technique has an important limitation: phylogenetic non-independence exists among taxa, violating the statistical assumptions underlying traditional meta-analytic models. Recently, meta-analytical techniques incorporating phylogenetic information have been developed to address this issue. However, ...

MOTIVATION In recent years there has been increased interest in producing large and accurate phylogenetic trees using statistical approaches. However for a large number of taxa, it is not feasible to construct large and accurate trees using only a single processor. A number of specialized parallel programs have been produced in an attempt to address the huge computational requirements of maximu...

Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny pr...

The gap between the amount of genome information released by genome sequencing projects and our knowledge about the proteins' functions is rapidly increasing. To fill this gap, various 'genomic-context' methods have been proposed that exploit sequenced genomes to predict the functions of the encoded proteins. One class of methods, phylogenetic profiling, predicts protein function by correlating...